diff --git a/.gitignore b/.gitignore index 0b6e57f..9c59327 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,9 @@ # Created by .ignore support plugin (hsz.mobi) ### Python template +# Custom +proc/* +.DS_Store + # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] diff --git a/README.md b/README.md index a9a2971..c906267 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,6 @@ -# Phigaro v2.3.0 +# Phigaro v2.4.0 [![PyPI version](https://badge.fury.io/py/phigaro.svg)](https://badge.fury.io/py/phigaro) -![Conda installation](https://anaconda.org/bioconda/phigaro/badges/installer/conda.svg) -![Actions Status](https://github.com/bobeobibo/phigaro/workflows/Phigaro%20Tests/badge.svg) +![Conda installation](https://anaconda.org/bioconda/phigaro/badges/version.svg) ![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) diff --git a/deployment.sh b/deployment.sh new file mode 100755 index 0000000..7b4b2b0 --- /dev/null +++ b/deployment.sh @@ -0,0 +1,28 @@ +#!/bin/bash +conda activate main +pip install --upgrade twine +echo "Did you change git action and updated the package?" +read +git status +read +git pull +read +rm dist/* +python setup_version.py +python setup.py sdist bdist_wheel +read +git add --all +git status +read +read -p commit_name="Please, make up the commit name:" +tag=`cat tag_name` +git commit -m $commit_name +read +git tag $tag +read +git push +read +git push --tags +read +twine upload --repository phigaro dist/* +read \ No newline at end of file diff --git a/dist/phigaro-2.3.0-py2.py3-none-any.whl b/dist/phigaro-2.3.0-py2.py3-none-any.whl deleted file mode 100644 index 3fa6736..0000000 Binary files a/dist/phigaro-2.3.0-py2.py3-none-any.whl and /dev/null differ diff --git a/dist/phigaro-2.3.0.tar.gz b/dist/phigaro-2.3.0.tar.gz deleted file mode 100644 index 96cbe08..0000000 Binary files a/dist/phigaro-2.3.0.tar.gz and /dev/null differ diff --git a/dist/phigaro-2.4.0-py2.py3-none-any.whl b/dist/phigaro-2.4.0-py2.py3-none-any.whl new file mode 100644 index 0000000..5624cbf Binary files /dev/null and b/dist/phigaro-2.4.0-py2.py3-none-any.whl differ diff --git a/dist/phigaro-2.4.0.tar.gz b/dist/phigaro-2.4.0.tar.gz new file mode 100644 index 0000000..21ffce9 Binary files /dev/null and b/dist/phigaro-2.4.0.tar.gz differ diff --git a/environment.yml b/environment.yml index ecf699d..47f7bbf 100644 --- a/environment.yml +++ b/environment.yml @@ -1,6 +1,6 @@ name: phigaro_env dependencies: - - python=3.7 + - python<=3.12.1 - pip - bioconda::prodigal - bioconda::hmmer diff --git a/phigaro/_version.py b/phigaro/_version.py index 8c402aa..2386b50 100644 --- a/phigaro/_version.py +++ b/phigaro/_version.py @@ -1,4 +1,4 @@ """Version information.""" # The following line *must* be the last in the module, exactly as formatted: -__version__ ="2.3.0" +__version__ ="2.4.0" diff --git a/phigaro/batch/task/base.py b/phigaro/batch/task/base.py index 320e96c..6dfeb09 100644 --- a/phigaro/batch/task/base.py +++ b/phigaro/batch/task/base.py @@ -14,9 +14,7 @@ class AbstractTask(object): def __init__(self): if self.task_name is None: - raise Exception( - "{}.task_name must by set".format(self.__class__.__name__) - ) + raise Exception("{}.task_name must by set".format(self.__class__.__name__)) self.directory() self.context = Context.instance() diff --git a/phigaro/batch/task/dummy.py b/phigaro/batch/task/dummy.py index 2ecfc57..df7c298 100644 --- a/phigaro/batch/task/dummy.py +++ b/phigaro/batch/task/dummy.py @@ -4,12 +4,12 @@ class DummyTask(AbstractTask): - task_name = 'dummy' + task_name = "dummy" def __init__(self, output, old_task_name): super().__init__() self._output = output - self.task_name = '{}-dummy'.format(old_task_name) + self.task_name = "{}-dummy".format(old_task_name) def run(self): pass diff --git a/phigaro/batch/task/gene_mark.py b/phigaro/batch/task/gene_mark.py index 508b90f..364adeb 100644 --- a/phigaro/batch/task/gene_mark.py +++ b/phigaro/batch/task/gene_mark.py @@ -7,19 +7,20 @@ class GeneMarkTask(AbstractTask): - task_name = 'gene_mark' + task_name = "gene_mark" def __init__(self, input): super().__init__() self.input = input - self._lst_file = input + '.lst' - self.gene_mark = sh.Command(self.config['genemark']['bin']).bake( - m=self.config['genemark']['mod_path'], A=self.output(), + self._lst_file = input + ".lst" + self.gene_mark = sh.Command(self.config["genemark"]["bin"]).bake( + m=self.config["genemark"]["mod_path"], + A=self.output(), ) def output(self): - return self.file('{}.faa'.format(self.sample)) + return self.file("{}.faa".format(self.sample)) def run(self): self.gene_mark(self.input) diff --git a/phigaro/batch/task/hmmer.py b/phigaro/batch/task/hmmer.py index 2e18a3d..3011dbc 100644 --- a/phigaro/batch/task/hmmer.py +++ b/phigaro/batch/task/hmmer.py @@ -7,7 +7,7 @@ class HmmerTask(AbstractTask): - task_name = 'hmmer' + task_name = "hmmer" def __init__(self, prodigal_task): """ @@ -18,18 +18,18 @@ def __init__(self, prodigal_task): self.prodigal = prodigal_task def _prepare(self): - self.hmmer = sh.Command(self.config['hmmer']['bin']) + self.hmmer = sh.Command(self.config["hmmer"]["bin"]) def output(self): - return self.file('{}.hmmer_out'.format(self.sample)) + return self.file("{}.hmmer_out".format(self.sample)) def run(self): self.hmmer( - '--cpu', + "--cpu", self.context.threads, - '--notextw', - '--tblout', + "--notextw", + "--tblout", self.output(), - self.config['hmmer']['pvog_path'], + self.config["hmmer"]["pvog_path"], self.prodigal.output(), ) diff --git a/phigaro/batch/task/parse_hmmer.py b/phigaro/batch/task/parse_hmmer.py index 2cb7301..a909154 100644 --- a/phigaro/batch/task/parse_hmmer.py +++ b/phigaro/batch/task/parse_hmmer.py @@ -10,11 +10,11 @@ logger = logging.getLogger(__name__) -INFINITY = float('inf') +INFINITY = float("inf") class ParseHmmerTask(AbstractTask): - task_name = 'parse_hmmer' + task_name = "parse_hmmer" def __init__(self, hmmer_task, gene_mark_task): """ @@ -27,27 +27,27 @@ def __init__(self, hmmer_task, gene_mark_task): self.genemark_task = gene_mark_task def output(self): - return self.file('{}.npn'.format(self.sample)) + return self.file("{}.npn".format(self.sample)) def run(self): self._parse_hmmer_output() @staticmethod def parse_line(line): - tokens = re.split(r'\s+', line) - scaffold = '>' + line.split('>')[1] + tokens = re.split(r"\s+", line) + scaffold = ">" + line.split(">")[1] name = tokens[0] evalue = float(tokens[4]) return scaffold, name, evalue def _parse_hmmer_output(self): - max_evalue = self.config['hmmer']['e_value_threshold'] + max_evalue = self.config["hmmer"]["e_value_threshold"] with open(self.hmmer_task.output()) as f: lines_it = ( self.parse_line(line.strip()) for line in f - if not line.startswith('#') and line.strip() + if not line.startswith("#") and line.strip() ) hmm_res = {} @@ -63,12 +63,10 @@ def _parse_hmmer_output(self): hmm_res[scaffold][gene_name] = evalue with open(self.genemark_task.output()) as f: - with open(self.output(), 'w') as of: - writer = csv.writer(of, delimiter='\t') + with open(self.output(), "w") as of: + writer = csv.writer(of, delimiter="\t") lines_it = ( - line.strip().split('\t') - for line in f - if line.startswith('>') + line.strip().split("\t") for line in f if line.startswith(">") ) for scaffold, group in groupby(lines_it, key=lambda t: t[1]): @@ -81,7 +79,5 @@ def _parse_hmmer_output(self): for gene_name, _ in group ) - is_phage_it = ( - 'P' if is_phage else 'N' for is_phage in is_phage_it - ) - writer.writerow((scaffold, ''.join(is_phage_it))) + is_phage_it = ("P" if is_phage else "N" for is_phage in is_phage_it) + writer.writerow((scaffold, "".join(is_phage_it))) diff --git a/phigaro/batch/task/path.py b/phigaro/batch/task/path.py index 36db2fc..d5afa70 100644 --- a/phigaro/batch/task/path.py +++ b/phigaro/batch/task/path.py @@ -5,15 +5,15 @@ def sample_name(sample_path): sample_path = basename(sample_path) - tokens = sample_path.split('.') + tokens = sample_path.split(".") if len(tokens) == 1: return sample_path else: - return '.'.join(tokens[:-1]) + return ".".join(tokens[:-1]) def path(*items): - items = ('proc',) + items + items = ("proc",) + items return join(*items) diff --git a/phigaro/batch/task/preprocess.py b/phigaro/batch/task/preprocess.py index 2a18cb1..b2fc6f4 100644 --- a/phigaro/batch/task/preprocess.py +++ b/phigaro/batch/task/preprocess.py @@ -6,7 +6,7 @@ class PreprocessTask(AbstractTask): - task_name = 'input_file' + task_name = "input_file" def __init__(self, input): super().__init__() @@ -15,8 +15,8 @@ def __init__(self, input): def check_fastafile(self): def get_users_answer(question): - yes = ['yes', 'y'] - no = ['no', 'n'] + yes = ["yes", "y"] + no = ["no", "n"] try: input_ = raw_input except NameError: @@ -40,20 +40,20 @@ def get_users_answer(question): SeqIO.write(records_to_save, self.output(), "fasta") del records_to_save - if not self.config['phigaro']['delete_shorts']: + if not self.config["phigaro"]["delete_shorts"]: if len(sequences_to_delete) > 0: print( - 'Error! Your fasta file contains at least one sequence length < 20000. The short sequences are: ' + "Error! Your fasta file contains at least one sequence length < 20000. The short sequences are: " ) - print('\n'.join(sequences_to_delete)) + print("\n".join(sequences_to_delete)) if not get_users_answer( - 'Do you want to start Phigaro without these sequences?' + "Do you want to start Phigaro without these sequences?" ): self.clean() exit(1) def output(self): - return self.file('{}.fasta'.format(self.sample)) + return self.file("{}.fasta".format(self.sample)) def run(self): self.check_fastafile() diff --git a/phigaro/batch/task/prodigal.py b/phigaro/batch/task/prodigal.py index 79fad98..e2ba757 100644 --- a/phigaro/batch/task/prodigal.py +++ b/phigaro/batch/task/prodigal.py @@ -5,18 +5,18 @@ class ProdigalTask(AbstractTask): - task_name = 'prodigal' + task_name = "prodigal" def __init__(self, preprocess_task): super().__init__() self.preprocess_task = preprocess_task - self.prodigal = sh.Command(self.config['prodigal']['bin']).bake( + self.prodigal = sh.Command(self.config["prodigal"]["bin"]).bake( i=self.preprocess_task.output(), a=self.output() ) def output(self): - return self.file('{}.faa'.format(self.sample)) + return self.file("{}.faa".format(self.sample)) def run(self): self.prodigal() diff --git a/phigaro/batch/task/run_phigaro.py b/phigaro/batch/task/run_phigaro.py index f35bf61..d085ed1 100644 --- a/phigaro/batch/task/run_phigaro.py +++ b/phigaro/batch/task/run_phigaro.py @@ -25,7 +25,7 @@ class RunPhigaroTask(AbstractTask): - task_name = 'run_phigaro' + task_name = "run_phigaro" def __init__(self, hmmer_task, prodigal_task): """ @@ -37,39 +37,35 @@ def __init__(self, hmmer_task, prodigal_task): self.prodigal_task = prodigal_task def _prepare(self): - self.mode = self.config['phigaro']['mode'] + self.mode = self.config["phigaro"]["mode"] self.finder = V2Finder( - window_len=self.config['phigaro']['window_len'], - threshold_min=self.config['phigaro'][ - 'threshold_min_%s' % self.mode - ], - threshold_max=self.config['phigaro'][ - 'threshold_max_%s' % self.mode - ], + window_len=self.config["phigaro"]["window_len"], + threshold_min=self.config["phigaro"]["threshold_min_%s" % self.mode], + threshold_max=self.config["phigaro"]["threshold_max_%s" % self.mode], mode=self.mode, ) - self._wtp = self.config['phigaro'].get('wtp', False) - self._print_vogs = self.config['phigaro'].get('print_vogs', False) - self._filename = self.config['phigaro'].get('filename', False) - self._no_html = self.config['phigaro'].get('no_html', False) - self._not_open = self.config['phigaro'].get('not_open', False) - self._save_fasta = self.config['phigaro'].get('save_fasta', False) - self._output = self.config['phigaro'].get('output', False) + self._wtp = self.config["phigaro"].get("wtp", False) + self._print_vogs = self.config["phigaro"].get("print_vogs", False) + self._filename = self.config["phigaro"].get("filename", False) + self._no_html = self.config["phigaro"].get("no_html", False) + self._not_open = self.config["phigaro"].get("not_open", False) + self._save_fasta = self.config["phigaro"].get("save_fasta", False) + self._output = self.config["phigaro"].get("output", False) if self._wtp: - self._output_wtp = self.config['phigaro'].get('output_wtp', False) - self._uuid = self.config['phigaro'].get('uuid', False) + self._output_wtp = self.config["phigaro"].get("output_wtp", False) + self._uuid = self.config["phigaro"].get("uuid", False) self.context = Context.instance() def output(self): - return self.file('{}.tsv'.format(self.sample)) + return self.file("{}.tsv".format(self.sample)) def run(self): - max_evalue = self.config['hmmer']['e_value_threshold'] - penalty_black = self.config['phigaro']['penalty_black'] - penalty_white = self.config['phigaro']['penalty_white'] - gff = self.config['phigaro']['gff'] - bed = self.config['phigaro']['bed'] - mean_gc = self.config['phigaro']['mean_gc'] + max_evalue = self.config["hmmer"]["e_value_threshold"] + penalty_black = self.config["phigaro"]["penalty_black"] + penalty_white = self.config["phigaro"]["penalty_white"] + gff = self.config["phigaro"]["gff"] + bed = self.config["phigaro"]["bed"] + mean_gc = self.config["phigaro"]["mean_gc"] pvogs_black_list = const.DEFAULT_BLACK_LIST pvogs_white_list = const.DEFAULT_WHITE_LIST @@ -77,7 +73,7 @@ def run(self): scaffold_set = read_prodigal_output(self.prodigal_task.output()) hmmer_result = read_hmmer_output(self.hmmer_task.output()) - gff_base = ['##gff-version 3.2.1'] + gff_base = ["##gff-version 3.2.1"] gff_scaffold = [] gff_prophage = [] gff_gene = [] @@ -85,33 +81,34 @@ def run(self): bed_gene = [] wtp_output = [] - with open(self.output(), 'w') as of: - writer = csv.writer(of, delimiter='\t') + with open(self.output(), "w") as of: + writer = csv.writer(of, delimiter="\t") if self._print_vogs: writer.writerow( ( - 'scaffold', - 'begin', - 'end', - 'transposable', - 'taxonomy', - 'vog', + "scaffold", + "id", + "begin", + "end", + "transposable", + "taxonomy", + "vog", ) ) else: writer.writerow( - ('scaffold', 'begin', 'end', 'transposable', 'taxonomy') + ("scaffold", "id", "begin", "end", "transposable", "taxonomy") ) plotly_plots = [] phage_info = [] transposables_status = [] - phage_num = 0 for scaffold in scaffold_set: + phage_num = 0 if gff: gff_scaffold.append( - '##sequence-region %s 1 %d' + "##sequence-region %s 1 %d" % ( scaffold.name, self.context.scaffolds_info[scaffold.name], @@ -128,119 +125,118 @@ def run(self): pvogs_black_list=pvogs_black_list, pvogs_white_list=pvogs_white_list, ) - gc = hmmer_res_to_gc( - scaffold, hmmer_result, max_evalue=max_evalue - ) - if self.mode == 'abs': + gc = hmmer_res_to_gc(scaffold, hmmer_result, max_evalue=max_evalue) + if self.mode == "abs": gc = np.array(gc) gc = np.absolute(gc - mean_gc) + mean_gc gc[gc == np.absolute(0 - mean_gc) + mean_gc] = 0 phages = self.finder.find_phages(npn, gc) + for phage in phages: phage_num += 1 - begin = genes[phage.begin].begin - end = genes[phage.end].end + phage_name = "%s_prophage%d" % (scaffold.name, phage_num) + begin = genes[phage.begin].begin - 1 + end = genes[phage.end].end - 1 phage_genes = genes[phage.begin : (phage.end + 1)] + + hmmer_records = [ + hmmer_result.min_record( + hmmer_result.get_records(scaffold.name, gene.name) + ) + for gene in genes[phage.begin : phage.end] + ] + hmmer_pvogs_records = ( + record.vog_name + for record in hmmer_records + if record and record.evalue <= max_evalue + ) + pvogs_records_str = ", ".join(hmmer_pvogs_records) + taxonomy = define_taxonomy(pvogs_records_str) + hmmer_records = [ + record + for record in hmmer_records + if record and record.evalue <= max_evalue + ] + transposable = if_transposable(hmmer_records) + if gff: gff_prophage.append( - '\t'.join( + "\t".join( [ scaffold.name, - '.', - 'prophage', + ".", + "prophage", str(begin + 1), str(end + 1), - '.', - '.', - '.', - 'ID=prophage%d' % phage_num, + ".", + ".", + ".", + "ID=%s;taxonomy=%s;transposable=%s" + % (phage_name, taxonomy, transposable), ] ) ) if bed: bed_prophage.append( - '\t'.join( + "\t".join( [ scaffold.name, str(begin), - str(end), - 'prophage%d' % phage_num, - '.', - '.', + str(end + 1), + phage_name, + ".", + ".", ] ) ) - hmmer_records = [ - hmmer_result.min_record( - hmmer_result.get_records(scaffold.name, gene.name) - ) - for gene in genes[phage.begin : phage.end] - ] + if gff or bed: for record in phage_genes: hmmer_record = hmmer_result.min_record( - hmmer_result.get_records( - scaffold.name, record.name - ) + hmmer_result.get_records(scaffold.name, record.name) ) pvog = ( - '.' - if hmmer_record is None - else hmmer_record.vog_name + "." if hmmer_record is None else hmmer_record.vog_name ) evalue = ( - '.' - if hmmer_record is None - else hmmer_record.evalue + "." if hmmer_record is None else hmmer_record.evalue ) if gff: gff_gene.append( - '\t'.join( + "\t".join( [ scaffold.name, - '.', - 'gene', - str(record.begin + 1), - str(record.end + 1), + ".", + "gene", + str(record.begin), + str(record.end), str(evalue), - '+' if record.strand > 0 else '-', - '.', - 'ID=gene%s;Parent=prophage%d;pvog=%s' - % (record.name, phage_num, pvog), + "+" if record.strand > 0 else "-", + ".", + "ID=%s;Parent=%s;pvog=%s" + % (record.name, phage_name, pvog), ] ) ) if bed: bed_gene.append( - '\t'.join( + "\t".join( [ scaffold.name, - str(record.begin), - str(record.end + 1), - 'gene%s' % (record.name), + str(record.begin - 1), + str(record.end), + record.name, str(evalue), - '+' if record.strand > 0 else '-', + "+" if record.strand > 0 else "-", ] ) ) - hmmer_pvogs_records = ( - record.vog_name - for record in hmmer_records - if record and record.evalue <= max_evalue - ) - pvogs_records_str = ', '.join(hmmer_pvogs_records) - taxonomy = define_taxonomy(pvogs_records_str) - hmmer_records = [ - record - for record in hmmer_records - if record and record.evalue <= max_evalue - ] - transposable = if_transposable(hmmer_records) if self._print_vogs: writer.writerow( ( scaffold.name, + phage_name, begin, end, transposable, @@ -250,12 +246,19 @@ def run(self): ) else: writer.writerow( - (scaffold.name, begin, end, transposable, taxonomy) + ( + scaffold.name, + phage_name, + begin, + end, + transposable, + taxonomy, + ) ) sequence, record = form_sequence( self._filename, - '%s_prophage_%d' % (scaffold.name, phage_num), + "%s_prophage_%d" % (scaffold.name, phage_num), begin, end, scaffold.name, @@ -270,48 +273,37 @@ def run(self): ] phage_info[-1][1].append(the_phage_info) if self._save_fasta: - with open(self._output + '.fasta', 'a') as f: + with open(self._output + ".fasta", "a") as f: SeqIO.write( SeqRecord( record, - id='%s_prophage_%d' - % (scaffold.name, phage_num), - description='%s_prophage_%d' + id=phage_name, + description="%s_prophage_%d" % (scaffold.name, phage_num), ), f, "fasta", ) if (not self._no_html) and (self._output): - plotly_plots.append( - plot_html(hmmer_records, begin, end) - ) - - + plotly_plots.append(plot_html(hmmer_records, begin, end)) phage_info = ( - phage_info - if len(phage_info[-1][1]) > 0 - else phage_info[:-1] + phage_info if len(phage_info[-1][1]) > 0 else phage_info[:-1] ) wtp_output = [the_phage_info[0] for the_phage_info in phage_info] if self._wtp: - with open(self._output_wtp, 'w') as f: - f.write( - '\n'.join(wtp_output) - ) + with open(self._output_wtp, "w") as f: + f.write("\n".join(wtp_output)) if gff: - with open(self._output + '.gff3', 'w') as f: + with open(self._output + ".gff3", "w") as f: f.write( - '\n'.join( - gff_base + gff_scaffold + gff_prophage + gff_gene - ) + "\n".join(gff_base + gff_scaffold + gff_prophage + gff_gene) ) if bed: - with open(self._output + '.bed', 'w') as f: - f.write('\n'.join(gff_base + bed_prophage + bed_gene)) + with open(self._output + ".bed", "w") as f: + f.write("\n".join(gff_base + bed_prophage + bed_gene)) if (len(phage_info) > 0) and (not self._no_html) and (self._output): html = form_html_document( @@ -321,12 +313,12 @@ def run(self): self._filename, self._uuid, ) - with open(self._output + '.html', 'w') as f: + with open(self._output + ".html", "w") as f: f.write(html) if not self._not_open: os.system( - 'xdg-open ' + "xdg-open " + self._output - + '.html' - + ' > /dev/null 2>/dev/null' + + ".html" + + " > /dev/null 2>/dev/null" ) diff --git a/phigaro/cli/batch.py b/phigaro/cli/batch.py index 0cdb931..0303f99 100644 --- a/phigaro/cli/batch.py +++ b/phigaro/cli/batch.py @@ -35,7 +35,7 @@ def create_task(substitutions, task_class, *args, **kwargs): task = task_class(*args, **kwargs) if task.task_name in substitutions: print( - 'Substituting output for {}: {}'.format( + "Substituting output for {}: {}".format( task.task_name, substitutions[task.task_name].output() ) ) @@ -46,7 +46,7 @@ def create_task(substitutions, task_class, *args, **kwargs): def clean_fold(): is_empty = True - for root, dirs, files in os.walk('proc', topdown=False): + for root, dirs, files in os.walk("proc", topdown=False): for name in files: is_empty = False break @@ -54,174 +54,174 @@ def clean_fold(): for name in dirs: os.rmdir(os.path.join(root, name)) if is_empty: - os.rmdir('proc') + os.rmdir("proc") def main(): - default_config_path = join(os.getenv('HOME'), '.phigaro', 'config.yml') + default_config_path = join(os.getenv("HOME"), ".phigaro", "config.yml") parser = argparse.ArgumentParser( - prog='phigaro', - description='Phigaro is a scalable command-line tool for predictions phages and prophages ' - 'from nucleid acid sequences', + prog="phigaro", + description="Phigaro is a scalable command-line tool for predictions phages and prophages " + "from nucleid acid sequences", ) parser.add_argument( - '-V', - '--version', - action='version', - version='%(prog)s {version}'.format(version=__version__), + "-V", + "--version", + action="version", + version="%(prog)s {version}".format(version=__version__), ) parser.add_argument( - '-f', - '--fasta-file', - help='Assembly scaffolds/contigs or full genomes, required', + "-f", + "--fasta-file", + help="Assembly scaffolds/contigs or full genomes, required", required=True, ) parser.add_argument( - '-c', - '--config', + "-c", + "--config", default=default_config_path, - help='Path to the config file, not required. The deafult is %s'%default_config_path, + help="Path to the config file, not required. The deafult is %s" + % default_config_path, ) + parser.add_argument("-v", "--verbose", action="store_true", help=argparse.SUPPRESS) parser.add_argument( - '-v', '--verbose', action='store_true', help=argparse.SUPPRESS + "-p", + "--print-vogs", + help="Print phage vogs for each region", + action="store_true", ) parser.add_argument( - '-p', - '--print-vogs', - help='Print phage vogs for each region', - action='store_true', + "-e", + "--extension", + default=["html"], + nargs="+", + help="Type of the output: html, tsv, gff, bed or stdout. Default is html. You can specify several file formats with a space as a separator. Example: -e tsv html stdout.", ) parser.add_argument( - '-e', - '--extension', - default=['html'], - nargs='+', - help='Type of the output: html, tsv, gff, bed or stdout. Default is html. You can specify several file formats with a space as a separator. Example: -e tsv html stdout.', + "-o", + "--output", + default="", + help="Output filename for html and txt outputs. Required by default, but not required for stdout only output.", ) parser.add_argument( - '-o', - '--output', - default='', - help='Output filename for html and txt outputs. Required by default, but not required for stdout only output.', + "--not-open", + help="Do not open html file automatically, if html output type is specified.", + action="store_true", ) parser.add_argument( - '--not-open', - help='Do not open html file automatically, if html output type is specified.', - action='store_true', - ) - parser.add_argument( - '-t', - '--threads', + "-t", + "--threads", type=int, default=multiprocessing.cpu_count(), - help='Num of threads (' - 'default is num of CPUs={})'.format(multiprocessing.cpu_count()), + help="Num of threads (" + "default is num of CPUs={})".format(multiprocessing.cpu_count()), ) parser.add_argument( - '--no-cleanup', action='store_true', help="Do not delete any temporary files that was generated by Phigaro (HMMER & Prodigal outputs and some others)." + "--no-cleanup", + action="store_true", + help="Do not delete any temporary files that was generated by Phigaro (HMMER & Prodigal outputs and some others).", ) parser.add_argument( - '-S', - '--substitute-output', - action='append', - help='If you have precomputed prodigal and/or hmmer data you can provide paths to the files in the following format: program:address/to/the/file. In place of program you should write hmmer or prodigal. If you need to provide both files you should pass them separetely as two parametres.', + "-S", + "--substitute-output", + action="append", + help="If you have precomputed prodigal and/or hmmer data you can provide paths to the files in the following format: program:address/to/the/file. In place of program you should write hmmer or prodigal. If you need to provide both files you should pass them separetely as two parametres.", ) parser.add_argument( - '--save-fasta', - action='store_true', - help='Save all phage fasta sequences in a fasta file.', + "--save-fasta", + action="store_true", + help="Save all phage fasta sequences in a fasta file.", ) parser.add_argument( - '-d', - '--delete-shorts', - action='store_true', - help='Exclude sequences with length < 20000 automatically.', + "-d", + "--delete-shorts", + action="store_true", + help="Exclude sequences with length < 20000 automatically.", ) parser.add_argument( - '-m', - '--mode', - default='basic', - help='You can launch Phigaro at one of 3 modes: basic, abs, without_gc. Default is basic. Read more about modes at https://github.com/bobeobibo/phigaro/', - ) - parser.add_argument( - '--wtp', - action='store_true', - help=argparse.SUPPRESS + "-m", + "--mode", + default="basic", + help="You can launch Phigaro at one of 3 modes: basic, abs, without_gc. Default is basic. Read more about modes at https://github.com/bobeobibo/phigaro/", ) + parser.add_argument("--wtp", action="store_true", help=argparse.SUPPRESS) args = parser.parse_args() logging.basicConfig(level=logging.INFO if args.verbose else logging.WARN) - logging.getLogger('sh.command').setLevel(logging.WARN) + logging.getLogger("sh.command").setLevel(logging.WARN) logger = logging.getLogger(__name__) if not exists(args.config): # TODO: pretty message - print('Please, create config file using phigaro-setup script') + print("Please, create config file using phigaro-setup script") exit(1) args.extension = [atype.lower() for atype in args.extension] for ext in args.extension: - if ext not in ['html', 'gff', 'bed', 'tsv', 'stdout']: + if ext not in ["html", "gff", "bed", "tsv", "stdout"]: print( - 'Error! The unknown output format in -e/--extensionn parameter: %s. Please, choose one or several from the list: html, gff, bed, tsv, stdout'%ext - ) + "Error! The unknown output format in -e/--extensionn parameter: %s. Please, choose one or several from the list: html, gff, bed, tsv, stdout" + % ext + ) exit(1) - if (args.output == '') and (args.extension != ['stdout']): + if (args.output == "") and (args.extension != ["stdout"]): print( - 'Error! Argument -o/--output is required or change the type of the output to stdout.' + "Error! Argument -o/--output is required or change the type of the output to stdout." ) exit(1) with open(args.config) as f: - logger.info('Using config file: {}'.format(args.config)) + logger.info("Using config file: {}".format(args.config)) config = yaml.load(f, Loader=yaml.FullLoader) - config['phigaro']['wtp'] = args.wtp - config['phigaro']['print_vogs'] = args.print_vogs - config['phigaro']['filename'] = args.fasta_file - config['phigaro']['no_html'] = ( - True if 'html' not in args.extension else False - ) - config['phigaro']['not_open'] = args.not_open - config['phigaro']['output'] = (args.output+'/'+os.path.splitext(os.path.basename(args.fasta_file))[0]+'.phigaro').replace('//', '/') - config['phigaro']['uuid'] = uuid.uuid4().hex - config['phigaro']['delete_shorts'] = args.delete_shorts - config['phigaro']['gff'] = True if ('gff' in args.extension) else False - config['phigaro']['bed'] = True if ('bed' in args.extension) else False - config['phigaro']['mode'] = args.mode - config['phigaro']['save_fasta'] = args.save_fasta + config["phigaro"]["wtp"] = args.wtp + config["phigaro"]["print_vogs"] = args.print_vogs + config["phigaro"]["filename"] = args.fasta_file + config["phigaro"]["no_html"] = True if "html" not in args.extension else False + config["phigaro"]["not_open"] = args.not_open + config["phigaro"]["output"] = ( + args.output + + "/" + + os.path.splitext(os.path.basename(args.fasta_file))[0] + + ".phigaro" + ).replace("//", "/") + config["phigaro"]["uuid"] = uuid.uuid4().hex + config["phigaro"]["delete_shorts"] = args.delete_shorts + config["phigaro"]["gff"] = True if ("gff" in args.extension) else False + config["phigaro"]["bed"] = True if ("bed" in args.extension) else False + config["phigaro"]["mode"] = args.mode + config["phigaro"]["save_fasta"] = args.save_fasta filename = args.fasta_file - sample = '{}-{}'.format(sample_name(filename), config['phigaro']['uuid']) + sample = "{}-{}".format(sample_name(filename), config["phigaro"]["uuid"]) if args.wtp: - config['phigaro']['not_open'] = True - config['phigaro']['gff'] = True - config['phigaro']['bed'] = True - args.extension.append('tsv') - config['phigaro']['delete_shorts'] = True - config['phigaro']['print_vogs'] = True - config['phigaro']['output_wtp'] = args.output + '/phigaro.txt' - config['phigaro']['output'] = args.output +'/phigaro/phigaro' - config['phigaro']['save_fasta'] = True - - - if config['phigaro']['output'] != '': - fold = os.path.dirname(config['phigaro']['output']) + config["phigaro"]["not_open"] = True + config["phigaro"]["gff"] = True + config["phigaro"]["bed"] = True + args.extension.append("tsv") + config["phigaro"]["delete_shorts"] = True + config["phigaro"]["print_vogs"] = True + config["phigaro"]["output_wtp"] = args.output + "/phigaro.txt" + config["phigaro"]["output"] = args.output + "/phigaro/phigaro" + config["phigaro"]["save_fasta"] = True + + if config["phigaro"]["output"] != "": + fold = os.path.dirname(config["phigaro"]["output"]) if fold and not os.path.isdir(fold): os.makedirs(fold) if args.wtp: - fold = os.path.dirname(config['phigaro']['output_wtp']) + fold = os.path.dirname(config["phigaro"]["output_wtp"]) if fold and not os.path.isdir(fold): os.makedirs(fold) - - Context.initialize( - sample=sample, config=config, threads=args.threads, + sample=sample, + config=config, + threads=args.threads, ) substitutions = parse_substitute_output(args.substitute_output) @@ -231,9 +231,7 @@ def main(): prodigal_task = create_task( substitutions, ProdigalTask, preprocess_task=preprocess_task ) - hmmer_task = create_task( - substitutions, HmmerTask, prodigal_task=prodigal_task - ) + hmmer_task = create_task(substitutions, HmmerTask, prodigal_task=prodigal_task) run_phigaro_task = create_task( substitutions, @@ -245,14 +243,14 @@ def main(): tasks = [preprocess_task, prodigal_task, hmmer_task, run_phigaro_task] task_output_file = run_tasks_chain(tasks) - if ('tsv' in args.extension) or ('stdout' in args.extension): + if ("tsv" in args.extension) or ("stdout" in args.extension): with open(task_output_file) as f: f = list(f) - if 'tsv' in args.extension: - out_f = open(config['phigaro']['output'] + '.tsv', 'w') + if "tsv" in args.extension: + out_f = open(config["phigaro"]["output"] + ".tsv", "w") for line in f: out_f.write(line) - if 'stdout' in args.extension: + if "stdout" in args.extension: out_f = sys.stdout for line in f: out_f.write(line) @@ -264,5 +262,5 @@ def main(): clean_fold() -if __name__ == '__main__': +if __name__ == "__main__": main() diff --git a/phigaro/cli/helper.py b/phigaro/cli/helper.py index 6b4a240..e7c17a7 100644 --- a/phigaro/cli/helper.py +++ b/phigaro/cli/helper.py @@ -21,23 +21,23 @@ def create_config(no_update_db, config_path, pvogs_dir, force): os.makedirs(config_dir) if exists(config_path) and not force: - print('Phigaro already configured') + print("Phigaro already configured") return helper = SetupHelper(no_update_db) try: config = helper.setup() # TODO: refactor 'allpvoghmms' const - config['hmmer']['pvog_path'] = os.path.join(pvogs_dir, 'allpvoghmms') + config["hmmer"]["pvog_path"] = os.path.join(pvogs_dir, "allpvoghmms") - print("Found Prodigal in: {}".format(config['prodigal']['bin'])) - print("Found HMMER in: {}".format(config['hmmer']['bin'])) - print("HMMER model in: {}".format(config['hmmer']['pvog_path'])) + print("Found Prodigal in: {}".format(config["prodigal"]["bin"])) + print("Found HMMER in: {}".format(config["hmmer"]["bin"])) + print("HMMER model in: {}".format(config["hmmer"]["pvog_path"])) - with open(config_path, 'w') as f: + with open(config_path, "w") as f: yaml.safe_dump(config, f, default_flow_style=False) except HelperException as ex: - sys.stdout.write(ex.message + '\n') + sys.stdout.write(ex.message + "\n") exit(1) return @@ -49,71 +49,69 @@ def read_config_and_download_pvogs(config_path): with open(config_path) as f: config = yaml.load(f, Loader=yaml.FullLoader) - pvogs_dir = dirname(config['hmmer']['pvog_path']) - print('Downloading models to {}'.format(pvogs_dir)) - download_pvogs('http://download.ripcm.com/phigaro/', pvogs_dir) + pvogs_dir = dirname(config["hmmer"]["pvog_path"]) + print("Downloading models to {}".format(pvogs_dir)) + download_pvogs("http://download.ripcm.com/phigaro/", pvogs_dir) def download_test_data(): test_data_dir = input( - 'Please, write a full path to the directory you want test data saved to' - + '(by default - working directory):' + "Please, write a full path to the directory you want test data saved to" + + "(by default - working directory):" ) - if test_data_dir == '': + if test_data_dir == "": test_data_dir = os.getcwd() - test_data_dir = test_data_dir.replace('\\', '/') + test_data_dir = test_data_dir.replace("\\", "/") test_data_dir = ( - test_data_dir + '/test_data' - if (test_data_dir[-1] != '/') - else test_data_dir + 'test_data' + test_data_dir + "/test_data" + if (test_data_dir[-1] != "/") + else test_data_dir + "test_data" ) - base_url = 'https://cdn.jsdelivr.net/gh/bobeobibo/phigaro/test_data/' + base_url = "https://cdn.jsdelivr.net/gh/bobeobibo/phigaro/test_data/" if not exists(test_data_dir): os.makedirs(test_data_dir) - download_file('Bacillus_anthracis_str_ames.fna', base_url, test_data_dir) - download_file('Bacillus_anthracis_str_ames.phg', base_url, test_data_dir) - download_file( - 'Bacillus_anthracis_str_ames.phg.html', base_url, test_data_dir - ) + download_file("Bacillus_anthracis_str_ames.fna", base_url, test_data_dir) + download_file("Bacillus_anthracis_str_ames.phg", base_url, test_data_dir) + download_file("Bacillus_anthracis_str_ames.phg.html", base_url, test_data_dir) def main(): - home = os.getenv('HOME') - phigaro_dir = os.path.join(home, '.phigaro') - phigaro_config = os.path.join(phigaro_dir, 'config.yml') - pvogs_dir = os.path.join(phigaro_dir, 'pvog') + home = os.getenv("HOME") + phigaro_dir = os.path.join(home, ".phigaro") + phigaro_config = os.path.join(phigaro_dir, "config.yml") + pvogs_dir = os.path.join(phigaro_dir, "pvog") parser = argparse.ArgumentParser( - prog='phigaro-setup', + prog="phigaro-setup", description="Phigaro setup helper", formatter_class=argparse.ArgumentDefaultsHelpFormatter, ) parser.add_argument( - '-c', - '--config', + "-c", + "--config", default=phigaro_config, - help='Path to a config.yml, default is {}'.format(phigaro_config), + help="Path to a config.yml, default is {}".format(phigaro_config), ) parser.add_argument( - '-p', - '--pvog', + "-p", + "--pvog", default=pvogs_dir, - help='pvogs directory, default is {}'.format(pvogs_dir), + help="pvogs directory, default is {}".format(pvogs_dir), ) parser.add_argument( - '-f', - '--force', - action='store_true', - help='Force configuration and rewrite config.yml if exists', + "-f", + "--force", + action="store_true", + help="Force configuration and rewrite config.yml if exists", ) parser.add_argument( - '--no-updatedb', action='store_true', help='Do not run sudo updatedb' + "--no-updatedb", action="store_true", help="Do not run sudo updatedb" ) # parser.add_argument('--download-models', action='store_true', help='Skip configuration step and download models') args = parser.parse_args() if args.force: - sh.rm('-rf', args.config) + sh.rm("-rf", args.config) create_config( no_update_db=args.no_updatedb, config_path=args.config, @@ -123,26 +121,26 @@ def main(): read_config_and_download_pvogs(args.config) while True: - overwrite = input('Do you want to download test data Y/N?') - if overwrite.upper() in {'Y', 'YES'}: - overwrite = 'Y' + overwrite = input("Do you want to download test data Y/N?") + if overwrite.upper() in {"Y", "YES"}: + overwrite = "Y" break - elif overwrite.upper() in {'N', 'NO'}: - overwrite = 'N' + elif overwrite.upper() in {"N", "NO"}: + overwrite = "N" break - if overwrite == 'Y': + if overwrite == "Y": download_test_data() - print('To run phigaro on test data enter the following command:') - print('') + print("To run phigaro on test data enter the following command:") + print("") print( - ' phigaro -f test_data/Bacillus_anthracis_str_ames.fna -o test_data/Bacillus_anthracis_str_ames.phg -p --not-open' + " phigaro -f test_data/Bacillus_anthracis_str_ames.fna -o test_data/Bacillus_anthracis_str_ames.phg -p --not-open" ) - print('') + print("") print( - 'The installation process is finished. If you have any questions, you can visit our github: https://github.com/bobeobibo/phigaro.' + "The installation process is finished. If you have any questions, you can visit our github: https://github.com/bobeobibo/phigaro." ) -if __name__ == '__main__': +if __name__ == "__main__": main() diff --git a/phigaro/cli/phigaro.py b/phigaro/cli/phigaro.py index a5ffb11..c94c07a 100644 --- a/phigaro/cli/phigaro.py +++ b/phigaro/cli/phigaro.py @@ -10,16 +10,16 @@ from phigaro.data import convert_npn -def find_and_print_phages(npn_filename, finder, sep='\t'): +def find_and_print_phages(npn_filename, finder, sep="\t"): # type: (str, AbstractFinder) -> list[(str, str, list[Phage])] - writer = csv.writer(sys.stdout, delimiter='\t') - writer.writerow(('scaffold', 'begin', 'end')) + writer = csv.writer(sys.stdout, delimiter="\t") + writer.writerow(("scaffold", "begin", "end")) with open(npn_filename) as f: reader = csv.reader(f, delimiter=sep) for scaffold, npn_str in reader: - npn = convert_npn(npn_str, 'P') + npn = convert_npn(npn_str, "P") phages = finder.find_phages(npn) for phage in phages: writer.writerow((scaffold, phage.begin, phage.end)) @@ -29,10 +29,10 @@ def main(): p = argparse.ArgumentParser( description="Tool for predicting prophages in metagenomes" ) - p.add_argument('npn_file') - p.add_argument('-w', '--window-len', default=const.DEFAULT_WINDOW_SIZE) - p.add_argument('-m', '--threshold-min', default=const.DEFAULT_THRESHOLD_MIN) - p.add_argument('-M', '--threshold-max', default=const.DEFAULT_THRESHOLD_MAX) + p.add_argument("npn_file") + p.add_argument("-w", "--window-len", default=const.DEFAULT_WINDOW_SIZE) + p.add_argument("-m", "--threshold-min", default=const.DEFAULT_THRESHOLD_MIN) + p.add_argument("-M", "--threshold-max", default=const.DEFAULT_THRESHOLD_MAX) args = p.parse_args() @@ -45,5 +45,5 @@ def main(): find_and_print_phages(args.npn_file, finder) -if __name__ == '__main__': +if __name__ == "__main__": main() diff --git a/phigaro/const.py b/phigaro/const.py index 25450f1..123b021 100644 --- a/phigaro/const.py +++ b/phigaro/const.py @@ -10,51 +10,51 @@ DEFAULT_PENALTY_BLACK = 2.2 DEFAULT_PENALTY_WHITE = 0.7 DEFAULT_BLACK_LIST = [ - 'VOG0496', - 'VOG5264', - 'VOG4730', - 'VOG5818', - 'VOG7281', - 'VOG6063', - 'VOG6030', - 'VOG1710', - 'VOG0996', - 'VOG4524', - 'VOG8021', - 'VOG8536', - 'VOG2368', - 'VOG1850', - 'VOG1031', - 'VOG0985', - 'VOG0274', - 'VOG4344', - 'VOG1844', - 'VOG0088', - 'VOG8607', - 'VOG4615', - 'VOG8992', - 'VOG3235', - 'VOG0092', - 'VOG4155', - 'VOG3532', - 'VOG1045', - 'VOG4149', - 'VOG8062', - 'VOG4562', - 'VOG7442', - 'VOG7446', - 'VOG0419', - 'VOG4319', - 'VOG8429', - 'VOG4409', - 'VOG1422', - 'VOG10018', - 'VOG3101', - 'VOG5441', - 'VOG4469', - 'VOG6988', - 'VOG4678', - 'VOG3722', + "VOG0496", + "VOG5264", + "VOG4730", + "VOG5818", + "VOG7281", + "VOG6063", + "VOG6030", + "VOG1710", + "VOG0996", + "VOG4524", + "VOG8021", + "VOG8536", + "VOG2368", + "VOG1850", + "VOG1031", + "VOG0985", + "VOG0274", + "VOG4344", + "VOG1844", + "VOG0088", + "VOG8607", + "VOG4615", + "VOG8992", + "VOG3235", + "VOG0092", + "VOG4155", + "VOG3532", + "VOG1045", + "VOG4149", + "VOG8062", + "VOG4562", + "VOG7442", + "VOG7446", + "VOG0419", + "VOG4319", + "VOG8429", + "VOG4409", + "VOG1422", + "VOG10018", + "VOG3101", + "VOG5441", + "VOG4469", + "VOG6988", + "VOG4678", + "VOG3722", ] DEFAULT_WHITE_LIST = [ "VOG0568", diff --git a/phigaro/data.py b/phigaro/data.py index 6039daa..9c41bcd 100644 --- a/phigaro/data.py +++ b/phigaro/data.py @@ -1,17 +1,17 @@ import csv import re -from collections import OrderedDict, defaultdict, Iterable +from collections import OrderedDict, defaultdict from itertools import groupby -import pickle +import json from phigaro.misc.ranges import first import numpy as np import os -INFINITY = float('inf') +INFINITY = float("inf") def read_npn(filename, sep=None, as_dict=True): - sep = sep or ' ' + sep = sep or " " with open(filename) as f: reader = csv.reader(f, delimiter=sep) if as_dict: @@ -21,7 +21,7 @@ def read_npn(filename, sep=None, as_dict=True): def read_coords(filename, sep=None): - sep = sep or '\t' + sep = sep or "\t" with open(filename) as f: reader = csv.reader(f, delimiter=sep) res = {} @@ -46,11 +46,10 @@ def hmmer_res_to_npn( pvogs_black_list, pvogs_white_list, ): + # type: (Scaffold, HmmerResult, float)->list[int] ordered_records_it = ( - HmmerResult.min_record( - hmmer_result.get_records(scaffold.name, gene.name) - ) + HmmerResult.min_record(hmmer_result.get_records(scaffold.name, gene.name)) for gene in scaffold ) @@ -69,9 +68,7 @@ def hmmer_res_to_npn( def hmmer_res_to_gc(scaffold, hmmer_result, max_evalue): # type: (Scaffold, HmmerResult, float)->list[int] ordered_records_it = ( - HmmerResult.min_record( - hmmer_result.get_records(scaffold.name, gene.name) - ) + HmmerResult.min_record(hmmer_result.get_records(scaffold.name, gene.name)) for gene in scaffold ) @@ -113,9 +110,7 @@ def get_gene(self, gene_name): class ScaffoldSet(object): def __init__(self, scaffolds): # type: (list[Scaffold])->ScaffoldSet - self._scaffolds_map = { - scaffold.name: scaffold for scaffold in scaffolds - } + self._scaffolds_map = {scaffold.name: scaffold for scaffold in scaffolds} def get_scaffold(self, scaffold_name): # type: (str)->Scaffold @@ -179,19 +174,19 @@ def read_hmmer_output(file_path): def parse_line(line): # type: (str)->HmmerRecord - tokens = re.split(r'\s+', line) - begin, end, strand = line.split(' # ', 4)[1:-1] + tokens = re.split(r"\s+", line) + begin, end, strand = line.split(" # ", 4)[1:-1] gc_cont = float( [ - x.split('=')[-1] - for x in tokens[-1].split(';') - if x.startswith('gc_cont') + x.split("=")[-1] + for x in tokens[-1].split(";") + if x.startswith("gc_cont") ][0] ) return HmmerRecord( - scaffold_name='_'.join(tokens[0].split('_')[:-1]), - gene_name=tokens[0].split('_')[-1], + scaffold_name="_".join(tokens[0].split("_")[:-1]), + gene_name=tokens[0], vog_name=tokens[2], evalue=float(tokens[4]), gc_cont=gc_cont, @@ -204,7 +199,7 @@ def parse_line(line): lines_it = ( parse_line(line.strip()) for line in f - if not line.startswith('#') and line.strip() + if not line.startswith("#") and line.strip() ) hmm_res = HmmerResult(lines_it) @@ -217,7 +212,7 @@ def read_prodigal_output(file_name): def extract_coords_and_name(gene_str): # type: (str)->Gene - tokens = gene_str.split(' # ') + tokens = gene_str.split(" # ") return Gene( name=tokens[0], begin=int(tokens[1]), @@ -227,45 +222,40 @@ def extract_coords_and_name(gene_str): def parse_gene_records(gene_records): # type: (list[str])->list[Gene] - return [ - extract_coords_and_name(gene_str) for _, gene_str in gene_records - ] + return [extract_coords_and_name(gene_str) for _, gene_str in gene_records] with open(file_name) as f: genes_scaffold_recs = ( [ - '_'.join(line.strip().split(' # ', 1)[0].split('_')[:-1]), - line.strip().split(' # ', 1)[0].split('_')[-1] - + ' # ' - + line.strip().split(' # ', 1)[1], + "_".join(line.strip().split(" # ", 1)[0].split("_")[:-1]), + line.strip().split(" # ", 1)[0].replace(">", "") + + " # " + + line.strip().split(" # ", 1)[1], ] for line in f - if line.startswith('>') + if line.startswith(">") ) scaffolds = [ - Scaffold( - name=scaffold_name[1:], genes=parse_gene_records(gene_records) - ) - for scaffold_name, gene_records in groupby( - genes_scaffold_recs, key=first - ) + Scaffold(name=scaffold_name[1:], genes=parse_gene_records(gene_records)) + for scaffold_name, gene_records in groupby(genes_scaffold_recs, key=first) ] return ScaffoldSet(scaffolds=scaffolds) def define_taxonomy(pvogs_string): with open( - os.path.dirname(os.path.abspath(__file__)) + '/pvogs_taxonomy.pickle', - 'rb', + os.path.dirname(os.path.abspath(__file__)) + "/pvogs_taxonomy.json", + "r", ) as f: - pvogs_taxonomy, taxonomy_codes = pickle.load(f) - taxonomy_codes = taxonomy_codes.astype(str) - pvog_list = pvogs_string.split(', ') + data = json.load(f) + pvogs_taxonomy = data["pvogs_taxonomy"] + taxonomy_codes = np.array(data["taxonomy_codes"]) + pvog_list = pvogs_string.split(", ") taxonomy_variants = [ pvogs_taxonomy[pvog] for pvog in pvog_list if pvog in pvogs_taxonomy ] if len(taxonomy_variants) > 0: taxonomies, counts = np.unique(taxonomy_variants, return_counts=True) - return ' / '.join(taxonomy_codes[taxonomies[counts == max(counts)]]) + return " / ".join(taxonomy_codes[taxonomies[counts == max(counts)]]) else: - return 'Unknown' + return "Unknown" diff --git a/phigaro/finder/v1.py b/phigaro/finder/v1.py index 84bab7c..c380754 100644 --- a/phigaro/finder/v1.py +++ b/phigaro/finder/v1.py @@ -18,9 +18,7 @@ def find_phages(self, bacteria_npn): kkz, ar_positions = convert_npn(bacteria_npn) grad = count_grad(kkz, self.window_size) - norm_grad = count_norm_grad( - grad, self.window_size, self.min_phage_in_window - ) + norm_grad = count_norm_grad(grad, self.window_size, self.min_phage_in_window) phages = get_phages(kkz, norm_grad) for phage in phages: @@ -30,9 +28,9 @@ def find_phages(self, bacteria_npn): # ) yield Phage( - begin=phage['start'], - end=phage['end'], - is_prophage=phage['end'] - phage['start'] < 0.8 * len(kkz), + begin=phage["start"], + end=phage["end"], + is_prophage=phage["end"] - phage["start"] < 0.8 * len(kkz), ) @@ -48,9 +46,7 @@ def count_grad(sequence, window_size): end = int(i + offset) if end > len(sequence) - 1: # if end is out of range end = len(sequence) - 1 - grad[i] += sum( - sequence[start : end + 1] - ) # count sum of elements in window + grad[i] += sum(sequence[start : end + 1]) # count sum of elements in window return grad @@ -128,10 +124,10 @@ def convert_npn(npn): ar_positions = [] for i, letter in enumerate(npn): - if letter == 'P': + if letter == "P": kkz.append(1) else: kkz.append(0) - if letter == 'r': + if letter == "r": ar_positions.append(i) return kkz, ar_positions diff --git a/phigaro/finder/v2.py b/phigaro/finder/v2.py index 0caecdc..657cfd3 100644 --- a/phigaro/finder/v2.py +++ b/phigaro/finder/v2.py @@ -19,7 +19,7 @@ def __init__(self, window_len, threshold_min, threshold_max, mode): def find_phages(self, bacteria_npn, bacteria_gc): scores = calc_scores(bacteria_npn, self.window_len) - if self.mode != 'without_gc': + if self.mode != "without_gc": gc_scores = calc_scores(bacteria_gc, self.window_len) ranges = scan_phages( np.array(scores) * np.array(gc_scores), @@ -32,7 +32,9 @@ def find_phages(self, bacteria_npn, bacteria_gc): ) for (begin, end) in ranges: yield Phage( - begin=begin, end=end, is_prophage=True, + begin=begin, + end=end, + is_prophage=True, ) diff --git a/phigaro/helper.py b/phigaro/helper.py index 9d5038b..a5869c2 100644 --- a/phigaro/helper.py +++ b/phigaro/helper.py @@ -24,9 +24,7 @@ class HMMERNotFound(HelperException): def _choose_option(message, options): - options = [s.rstrip() for s in options[:-1] if isfile(s.rstrip())] + [ - options[-1] - ] + options = [s.rstrip() for s in options[:-1] if isfile(s.rstrip())] + [options[-1]] if len(options) == 1: return options[0] @@ -36,28 +34,20 @@ def _choose_option(message, options): res = None for i, option in enumerate(options): print("[{}] {}".format(i + 1, option)) - option_num = input( - 'Choose your option (Enter for {}): '.format(options[0]) - ) - if option_num == '': - option_num = '1' - if re.match(r'^\d+$', option_num): + option_num = input("Choose your option (Enter for {}): ".format(options[0])) + if option_num == "": + option_num = "1" + if re.match(r"^\d+$", option_num): if int(option_num) == len(options): - which_program = ( - 'prodigal' if 'Prodigal' in message else 'hmmsearch' - ) - res = input( - 'Please, write a path to {}: '.format(which_program) - ) + which_program = "prodigal" if "Prodigal" in message else "hmmsearch" + res = input("Please, write a path to {}: ".format(which_program)) return res option_num = int(option_num) - 1 if 0 <= option_num < len(options): res = options[option_num] if res is None: print( - 'Please select valid option number ({} to {})'.format( - 1, len(options) - ) + "Please select valid option number ({} to {})".format(1, len(options)) ) continue return res @@ -68,31 +58,34 @@ def download_file(filename, base_url, out_dir): out = join(out_dir, filename) if exists(out): while True: - overwrite = input( - 'File {} already exists, overwrite it (Y/N)?'.format(out) - ) - if overwrite.upper() in {'Y', 'YES'}: - overwrite = 'Y' + overwrite = input("File {} already exists, overwrite it (Y/N)?".format(out)) + if overwrite.upper() in {"Y", "YES"}: + overwrite = "Y" break - elif overwrite.upper() in {'N', 'NO'}: - overwrite = 'N' + elif overwrite.upper() in {"N", "NO"}: + overwrite = "N" break - if overwrite == 'N': + if overwrite == "N": return - print('Downloading {url} to {out}'.format(url=url, out=out,)) - sh.wget('-O', out, url, _tty_out=True) + print( + "Downloading {url} to {out}".format( + url=url, + out=out, + ) + ) + sh.wget("-O", out, url, _tty_out=True) def download_pvogs(base_url, out_dir): if not exists(out_dir): os.makedirs(out_dir) # TODO: refactor 'allpvoghmms' const - download_file('allpvoghmms', base_url, out_dir) - download_file('allpvoghmms.h3f', base_url, out_dir) - download_file('allpvoghmms.h3i', base_url, out_dir) - download_file('allpvoghmms.h3m', base_url, out_dir) - download_file('allpvoghmms.h3p', base_url, out_dir) + download_file("allpvoghmms", base_url, out_dir) + download_file("allpvoghmms.h3f", base_url, out_dir) + download_file("allpvoghmms.h3i", base_url, out_dir) + download_file("allpvoghmms.h3m", base_url, out_dir) + download_file("allpvoghmms.h3p", base_url, out_dir) class SetupHelper(object): @@ -104,14 +97,14 @@ def _locate(self, *args, **kwargs): if not self._dont_update_db: try: print( - 'If you do not want to run sudo, use the following command to configure Phigaro:' + "If you do not want to run sudo, use the following command to configure Phigaro:" ) - print(' phigaro-setup --no-updatedb') + print(" phigaro-setup --no-updatedb") with sh.contrib.sudo: sh.updatedb() self._dont_update_db = True except sh.ErrorReturnCode_1: - print('Invalid password') + print("Invalid password") exit(1) try: return [s.rstrip() for s in sh.locate(*args, **kwargs)] @@ -119,8 +112,8 @@ def _locate(self, *args, **kwargs): return [] def _find_binary(self, name, options_message, raise_if_not_found): - locations = [sh.which(name) or ''] + self._locate( - '-b', '-r', '^{}$'.format(name) + locations = [sh.which(name) or ""] + self._locate( + "-b", "-r", "^{}$".format(name) ) locations = [l.rstrip() for l in locations if l.rstrip()] @@ -128,32 +121,37 @@ def _find_binary(self, name, options_message, raise_if_not_found): # raise raise_if_not_found() print(raise_if_not_found) which_program = ( - 'prodigal' if 'Prodigal' in raise_if_not_found else 'hmmsearch' + "prodigal" if "Prodigal" in raise_if_not_found else "hmmsearch" ) - locations = input('Write a full path to {}:'.format(which_program)) + locations = input("Write a full path to {}:".format(which_program)) return locations - locations.append('Add another path manually') - return _choose_option(message=options_message, options=locations,) + locations.append("Add another path manually") + return _choose_option( + message=options_message, + options=locations, + ) - def _setup_prodigal(self,): + def _setup_prodigal( + self, + ): prodigal_location = self._find_binary( - name='prodigal', - options_message='Please select appropriate Prodigal location', + name="prodigal", + options_message="Please select appropriate Prodigal location", raise_if_not_found=ProdigalNotFound.message, ) return { - 'bin': prodigal_location, + "bin": prodigal_location, } def _setup_hmmer(self): hmmsearch_location = self._find_binary( - name='hmmsearch', - options_message='Please select appropriate HMMER location', + name="hmmsearch", + options_message="Please select appropriate HMMER location", raise_if_not_found=HMMERNotFound.message, ) return { - 'bin': hmmsearch_location, + "bin": hmmsearch_location, } def setup(self): @@ -161,21 +159,23 @@ def setup(self): hmmer_params = self._setup_hmmer() return { - 'prodigal': {'bin': prodigal_params['bin'],}, - 'hmmer': { - 'bin': hmmer_params['bin'], - 'e_value_threshold': const.DEFAULT_MAX_EVALUE, + "prodigal": { + "bin": prodigal_params["bin"], + }, + "hmmer": { + "bin": hmmer_params["bin"], + "e_value_threshold": const.DEFAULT_MAX_EVALUE, }, - 'phigaro': { - 'window_len': const.DEFAULT_WINDOW_SIZE, - 'threshold_min_basic': const.DEFAULT_THRESHOLD_MIN_BASIC, - 'threshold_max_basic': const.DEFAULT_THRESHOLD_MAX_BASIC, - 'threshold_min_abs': const.DEFAULT_THRESHOLD_MIN_ABS, - 'threshold_max_abs': const.DEFAULT_THRESHOLD_MAX_ABS, - 'threshold_min_without_gc': const.DEFAULT_THRESHOLD_MIN_WITHOUT_GC, - 'threshold_max_without_gc': const.DEFAULT_THRESHOLD_MAX_WITHOUT_GC, - 'mean_gc': const.DEFAULT_MEAN_GC, - 'penalty_black': const.DEFAULT_PENALTY_BLACK, - 'penalty_white': const.DEFAULT_PENALTY_WHITE, + "phigaro": { + "window_len": const.DEFAULT_WINDOW_SIZE, + "threshold_min_basic": const.DEFAULT_THRESHOLD_MIN_BASIC, + "threshold_max_basic": const.DEFAULT_THRESHOLD_MAX_BASIC, + "threshold_min_abs": const.DEFAULT_THRESHOLD_MIN_ABS, + "threshold_max_abs": const.DEFAULT_THRESHOLD_MAX_ABS, + "threshold_min_without_gc": const.DEFAULT_THRESHOLD_MIN_WITHOUT_GC, + "threshold_max_without_gc": const.DEFAULT_THRESHOLD_MAX_WITHOUT_GC, + "mean_gc": const.DEFAULT_MEAN_GC, + "penalty_black": const.DEFAULT_PENALTY_BLACK, + "penalty_white": const.DEFAULT_PENALTY_WHITE, }, } diff --git a/phigaro/misc/ranges.py b/phigaro/misc/ranges.py index 046e871..1242d66 100644 --- a/phigaro/misc/ranges.py +++ b/phigaro/misc/ranges.py @@ -74,7 +74,7 @@ def jakkard_index(ranges1, ranges2): if intersection_len != 0 and union_len == 0: print(ranges1, ranges2) - raise Exception('union error') + raise Exception("union error") if intersection_len == 0: return 0 @@ -92,17 +92,13 @@ def minus(ranges1, ranges2): max_len = max(ranges1[-1][1], ranges2[-1][1]) + 1 ranges2 = intersection(ranges1, ranges2) ranges2 = negate(ranges2, max_len) - ranges2 = [ - (begin + 1, end - 1) for (begin, end) in ranges2 if end - begin >= 2 - ] + ranges2 = [(begin + 1, end - 1) for (begin, end) in ranges2 if end - begin >= 2] for (begin, end) in intersection(ranges1, ranges2): yield (begin, end) def true_positives_rate(test_ranges, real_ranges): - return len_ranges(intersection(test_ranges, real_ranges)) / len_ranges( - real_ranges - ) + return len_ranges(intersection(test_ranges, real_ranges)) / len_ranges(real_ranges) def false_positives_rate(test_ranges, real_ranges, max_len=None): diff --git a/phigaro/misc/vis.py b/phigaro/misc/vis.py index f7f9951..8707e9e 100644 --- a/phigaro/misc/vis.py +++ b/phigaro/misc/vis.py @@ -21,7 +21,12 @@ def plot_scores(scores, title, real_phage_coords=None): if real_phage_coords is not None: colors = _make_coords_colors(len(scores), real_phage_coords) data = Bar( - x=indices, y=scores + 0.1, name=title, marker=dict(color=colors,) + x=indices, + y=scores + 0.1, + name=title, + marker=dict( + color=colors, + ), ) return data @@ -30,23 +35,30 @@ def plot_scores(scores, title, real_phage_coords=None): def plot_phage(phage, title): ind = np.arange(len(phage)) int_phage = [c + 0.1 for c in phage] - data = Bar(x=ind, y=int_phage, marker=dict(color='black',), name=title) + data = Bar( + x=ind, + y=int_phage, + marker=dict( + color="black", + ), + name=title, + ) return data def _make_rects(coords, ymin, ymax, fillcolor, opacity): return [ dict( - type='rect', - xref='x', - yref='y', + type="rect", + xref="x", + yref="y", x0=x_begin, y0=ymin, x1=x_end, y1=ymax, fillcolor=fillcolor, opacity=opacity, - line={'width': 0}, + line={"width": 0}, ) for (x_begin, x_end) in coords ] @@ -57,7 +69,7 @@ def plot_scores_and_phage( ): score_func = score_func or score_tri fig = tools.make_subplots(rows=2, cols=1, shared_xaxes=True) - title = 'Scores: window: {}'.format(window_len) + title = "Scores: window: {}".format(window_len) scores = np.array(calc_scores(phage, window_len, score_func)) ranges = [] @@ -65,17 +77,17 @@ def plot_scores_and_phage( ranges = scan_func(scores) score_fig = plot_scores(scores, title, real_phage_coords=None) - phage_fig = plot_phage(phage, 'Phage') + phage_fig = plot_phage(phage, "Phage") fig.append_trace(score_fig, 1, 1) fig.append_trace(phage_fig, 2, 1) ymax = window_len / 2 if real_phage_coords is not None or ranges: - fig['layout'].update( + fig["layout"].update( dict( - shapes=_make_rects(ranges, ymax, 'rgb(50, 171, 96)', 0.5) - + _make_rects(real_phage_coords or [], ymax, '#ff0000', 0.5) + shapes=_make_rects(ranges, ymax, "rgb(50, 171, 96)", 0.5) + + _make_rects(real_phage_coords or [], ymax, "#ff0000", 0.5) ) ) @@ -87,14 +99,14 @@ def plot_scores_and_phage2( scores, found_phage_coords, real_phage_coords=None, - filename='filename', + filename="filename", ): # real_phage_coords = real_phage_coords or [] fig = tools.make_subplots(rows=2, cols=1, shared_xaxes=True) - title = 'Scores' + title = "Scores" score_fig = plot_scores(scores, title, real_phage_coords=None) - phage_fig = plot_phage(phage, 'Phage') + phage_fig = plot_phage(phage, "Phage") fig.append_trace(score_fig, 1, 1) fig.append_trace(phage_fig, 2, 1) @@ -103,15 +115,13 @@ def plot_scores_and_phage2( # print(len(real_phage_coords), len(found_phage_coords)) if (len(real_phage_coords) + len(found_phage_coords)) != 0: # print('got real coords') - fig['layout'].update( + fig["layout"].update( dict( shapes=_make_rects( - found_phage_coords, ymax * 0.5, ymax * 0.75, '#0000ff', 0.5 - ) - + _make_rects( - real_phage_coords, ymax * 0.75, ymax, '#aaaa00', 0.5 + found_phage_coords, ymax * 0.5, ymax * 0.75, "#0000ff", 0.5 ) + + _make_rects(real_phage_coords, ymax * 0.75, ymax, "#aaaa00", 0.5) ) ) - py.plot(fig, filename=filename + '.html') + py.plot(fig, filename=filename + ".html") diff --git a/phigaro/pvogs_taxonomy.json b/phigaro/pvogs_taxonomy.json new file mode 100644 index 0000000..d9b5228 --- /dev/null +++ b/phigaro/pvogs_taxonomy.json @@ -0,0 +1 @@ +{"pvogs_taxonomy": {"VOG1544": 1, "VOG1547": 1, "VOG0819": 1, "VOG1543": 1, "VOG0816": 1, "VOG0817": 1, "VOG0367": 0, "VOG0364": 0, "VOG0813": 1, "VOG0568": 0, "VOG0569": 0, "VOG0564": 1, "VOG0566": 0, "VOG0567": 0, "VOG0562": 1, "VOG1540": 1, "VOG4699": 0, "VOG2706": 1, "VOG2704": 1, "VOG2702": 1, "VOG2703": 1, "VOG2700": 1, "VOG2701": 1, "VOG1112": 1, "VOG0811": 1, "VOG0709": 0, "VOG1386": 2, "VOG1383": 0, "VOG1141": 1, "VOG1143": 1, "VOG1142": 1, "VOG1145": 1, "VOG1144": 1, "VOG1147": 1, "VOG1146": 1, "VOG1149": 1, "VOG1148": 1, "VOG0493": 0, "VOG0495": 0, "VOG0497": 0, "VOG2663": 1, "VOG0142": 0, "VOG0143": 0, "VOG0141": 0, "VOG0144": 0, "VOG0145": 0, "VOG0639": 2, "VOG3140": 0, "VOG0384": 0, "VOG5288": 0, "VOG5289": 0, "VOG0382": 0, "VOG2669": 1, "VOG5281": 0, "VOG0388": 0, "VOG0389": 0, "VOG5284": 0, "VOG5285": 0, "VOG5518": 0, "VOG5512": 0, "VOG5513": 0, "VOG5510": 0, "VOG5516": 0, "VOG5517": 0, "VOG5514": 0, "VOG5515": 0, "VOG4649": 1, "VOG4648": 1, "VOG4399": 0, "VOG5267": 0, "VOG5260": 1, "VOG5261": 0, "VOG5263": 0, "VOG4641": 1, "VOG4390": 0, 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-p2215 -I1 -sS'VOG0714' -p2216 -I1 -sS'VOG1175' -p2217 -I1 -sS'VOG1176' -p2218 -I1 -sS'VOG0488' -p2219 -I0 -sS'VOG1172' -p2220 -I1 -sS'VOG1173' -p2221 -I1 -sS'VOG0483' -p2222 -I0 -sS'VOG0482' -p2223 -I0 -sS'VOG0481' -p2224 -I0 -sS'VOG0480' -p2225 -I0 -sS'VOG0487' -p2226 -I0 -sS'VOG0486' -p2227 -I0 -sS'VOG0485' -p2228 -I0 -sS'VOG0484' -p2229 -I0 -sS'VOG5619' -p2230 -I0 -sS'VOG5618' -p2231 -I0 -sS'VOG5613' -p2232 -I4 -sS'VOG5612' -p2233 -I0 -sS'VOG5615' -p2234 -I2 -sS'VOG0396' -p2235 -I0 -sS'VOG0395' -p2236 -I0 -sS'VOG0394' -p2237 -I0 -sS'VOG5299' -p2238 -I1 -sS'VOG5298' -p2239 -I0 -sS'VOG0390' -p2240 -I0 -sS'VOG5294' -p2241 -I0 -sS'VOG5291' -p2242 -I0 -sS'VOG5290' -p2243 -I0 -sS'VOG5293' -p2244 -I1 -sS'VOG0398' -p2245 -I0 -sS'VOG5509' -p2246 -I0 -sS'VOG5505' -p2247 -I0 -sS'VOG5507' -p2248 -I0 -sS'VOG5506' -p2249 -I2 -sS'VOG5501' -p2250 -I0 -sS'VOG5503' -p2251 -I0 -sS'VOG5276' -p2252 -I1 -sS'VOG5275' -p2253 -I2 -sS'VOG5274' -p2254 -I1 -sS'VOG5273' -p2255 -I1 -sS'VOG5272' -p2256 -I0 -sS'VOG5271' -p2257 -I1 -sS'VOG4902' -p2258 -I0 -sS'VOG4903' -p2259 -I0 -sS'VOG4900' -p2260 -I0 -sS'VOG4901' -p2261 -I0 -sS'VOG4906' -p2262 -I0 -sS'VOG4907' -p2263 -I0 -sS'VOG4905' -p2264 -I0 -sS'VOG4273' -p2265 -I0 -sS'VOG4103' -p2266 -I0 -sS'VOG0029' -p2267 -I2 -sS'VOG4279' -p2268 -I0 -sS'VOG4876' -p2269 -I0 -sS'VOG4877' -p2270 -I0 -sS'VOG4874' -p2271 -I0 -sS'VOG4875' -p2272 -I1 -sS'VOG4870' -p2273 -I0 -sS'VOG4012' -p2274 -I0 -sS'VOG4013' -p2275 -I0 -sS'VOG4014' -p2276 -I0 -sS'VOG4015' -p2277 -I0 -sS'VOG4878' -p2278 -I0 -sS'VOG4017' -p2279 -I0 -sS'VOG5871' -p2280 -I0 -sS'VOG5870' -p2281 -I0 -sS'VOG5873' -p2282 -I1 -sS'VOG5875' -p2283 -I0 -sS'VOG5874' -p2284 -I1 -sS'VOG5877' -p2285 -I0 -sS'VOG5876' -p2286 -I0 -sS'VOG3614' -p2287 -I0 -sS'VOG5475' -p2288 -I1 -sS'VOG5474' -p2289 -I1 -sS'VOG5476' -p2290 -I0 -sS'VOG5471' -p2291 -I1 -sS'VOG5470' -p2292 -I1 -sS'VOG5473' -p2293 -I0 -sS'VOG5144' -p2294 -I0 -sS'VOG1984b' -p2295 -I0 -sS'VOG1984a' -p2296 -I0 -sS'VOG5479' -p2297 -I2 -sS'VOG5478' -p2298 -I1 -sS'VOG3129' -p2299 -I0 -sS'VOG4706' -p2300 -I0 -sS'VOG4707' -p2301 -I1 -sS'VOG4700' -p2302 -I0 -sS'VOG4701' -p2303 -I1 -sS'VOG4702' -p2304 -I0 -sS'VOG4703' -p2305 -I0 -sS'VOG1685' -p2306 -I0 -sS'VOG3125' -p2307 -I0 -sS'VOG4709' -p2308 -I0 -sS'VOG2063' -p2309 -I0 -sS'VOG2419' -p2310 -I0 -sS'VOG4691' -p2311 -I0 -sS'VOG3459' -p2312 -I1 -sS'VOG3058' -p2313 -I0 -sS'VOG3729' -p2314 -I2 -sS'VOG3055' -p2315 -I0 -sS'VOG3057' -p2316 -I0 -sS'VOG3056' -p2317 -I0 -sS'VOG3051' -p2318 -I1 -sS'VOG3050' -p2319 -I1 -sS'VOG2238' -p2320 -I0 -sS'VOG2899' -p2321 -I1 -sS'VOG2233' -p2322 -I4 -sS'VOG2894' -p2323 -I1 -sS'VOG2895' -p2324 -I1 -sS'VOG2892' -p2325 -I1 -sS'VOG2893' -p2326 -I1 -sS'VOG2890' -p2327 -I1 -sS'VOG2891' -p2328 -I1 -sS'VOG2526' -p2329 -I1 -sS'VOG2527' -p2330 -I1 -sS'VOG2522' -p2331 -I1 -sS'VOG2523' -p2332 -I1 -sS'VOG1968' -p2333 -I0 -sS'VOG1615' -p2334 -I1 -sS'VOG1614' -p2335 -I1 -sS'VOG1964' -p2336 -I0 -sS'VOG1611' -p2337 -I1 -sS'VOG1610' -p2338 -I1 -sS'VOG1613' -p2339 -I1 -sS'VOG2529' -p2340 -I1 -sS'VOG5246' -p2341 -I0 -sS'VOG5716' -p2342 -I1 -sS'VOG5243' -p2343 -I0 -sS'VOG2412' -p2344 -I0 -sS'VOG2413' -p2345 -I0 -sS'VOG2147' -p2346 -I1 -sS'VOG2417' -p2347 -I0 -sS'VOG2414' -p2348 -I0 -sS'VOG2415' -p2349 -I0 -sS'VOG2418' -p2350 -I0 -sS'VOG5241' -p2351 -I0 -sS'VOG3949' -p2352 -I1 -sS'VOG3943' -p2353 -I1 -sS'VOG3942' -p2354 -I1 -sS'VOG3941' -p2355 -I1 -sS'VOG3940' -p2356 -I1 -sS'VOG3947' -p2357 -I1 -sS'VOG3946' -p2358 -I1 -sS'VOG3944' -p2359 -I1 -sS'VOG2097' -p2360 -I2 -sS'VOG2094' -p2361 -I2 -sS'VOG2095' -p2362 -I2 -sS'VOG2098' -p2363 -I2 -scnumpy.core.multiarray -_reconstruct -p2364 -(cnumpy -ndarray -p2365 -(I0 -tp2366 -S'b' -p2367 -tp2368 -Rp2369 -(I1 -(I9 -tp2370 -cnumpy -dtype -p2371 -(S'S14' -p2372 -I0 -I1 -tp2373 -Rp2374 -(I3 -S'|' -p2375 -NNNI14 -I1 -I0 -tp2376 -bI00 -S'Myoviridae\x00\x00\x00\x00Siphoviridae\x00\x00Podoviridae\x00\x00\x00BicaudaviridaeMicroviridae\x00\x00Inoviridae\x00\x00\x00\x00FuselloviridaeTectiviridae\x00\x00Leviviridae\x00\x00\x00' -p2377 -tp2378 -btp2379 -. \ No newline at end of file diff --git a/phigaro/to_html/html_formation.py b/phigaro/to_html/html_formation.py index 7854abd..579d406 100644 --- a/phigaro/to_html/html_formation.py +++ b/phigaro/to_html/html_formation.py @@ -7,38 +7,32 @@ def form_html_document( ): def form_tbody(data, transposables_data): prophage_index = 1 - tbody = BeautifulSoup(features="lxml").new_tag('tbody') + tbody = BeautifulSoup(features="lxml").new_tag("tbody") for scaffold, scaffold_info in data: tr = BeautifulSoup(features="lxml").new_tag( - 'tr', **{'class': 'scaffold-name'} - ) - th = BeautifulSoup(features="lxml").new_tag( - 'th', scope="row", colspan="4" + "tr", **{"class": "scaffold-name"} ) + th = BeautifulSoup(features="lxml").new_tag("th", scope="row", colspan="4") th.append(scaffold) tr.append(th) tbody.append(tr) for prophage_info in scaffold_info: index_to_paste = ( BeautifulSoup( - transposable_index.format(prophage_index), 'html.parser' + transposable_index.format(prophage_index), "html.parser" ) if transposables_data[prophage_index - 1] else prophage_index ) if prophage_index == 1: prophage_info = ( - [prophage_index] - + prophage_info - + ['active', index_to_paste] + [prophage_index] + prophage_info + ["active", index_to_paste] ) else: prophage_info = ( - [prophage_index] + prophage_info + ['', index_to_paste] + [prophage_index] + prophage_info + ["", index_to_paste] ) - tbody.append( - BeautifulSoup(row.format(*prophage_info), 'html.parser') - ) + tbody.append(BeautifulSoup(row.format(*prophage_info), "html.parser")) prophage_index += 1 return str(tbody) @@ -47,27 +41,27 @@ def form_plots_body(data): for prophage_index, plot in enumerate(data): if prophage_index == 0: div = BeautifulSoup(features="lxml").new_tag( - 'div', + "div", **{ "class": "tab-pane fade show active", "id": "phage-%d" % (prophage_index + 1), } ) inner_div = BeautifulSoup(features="lxml").new_tag( - 'div', **{"class": "prophage-plot"} + "div", **{"class": "prophage-plot"} ) else: div = BeautifulSoup(features="lxml").new_tag( - 'div', + "div", **{ "class": "tab-pane fade show", "id": "phage-%d" % (prophage_index + 1), } ) inner_div = BeautifulSoup(features="lxml").new_tag( - 'div', **{"class": "prophage-plot", "style": "display:none"} + "div", **{"class": "prophage-plot", "style": "display:none"} ) - inner_div.append(BeautifulSoup(plot, 'html.parser')) + inner_div.append(BeautifulSoup(plot, "html.parser")) div.append(inner_div) plots_body.append(div) return str(plots_body) diff --git a/phigaro/to_html/html_templates.py b/phigaro/to_html/html_templates.py index 0fd9e45..3e04eb8 100644 --- a/phigaro/to_html/html_templates.py +++ b/phigaro/to_html/html_templates.py @@ -1,4 +1,4 @@ -header = ''' +header = """ Phigaro report: {0} @@ -7,8 +7,8 @@ - ''' -style_css = ''' + """ +style_css = """ - ''' + """ -body_main = ''' +body_main = """
{0} {1}
-''' +""" -body_table = '''
+body_table = """
@@ -441,11 +441,11 @@ -''' +""" -body_plots = '''
{0}
''' +body_plots = """
{0}
""" -transposable_index = '''
+transposable_index = """
@@ -455,9 +455,9 @@ {0}
-''' +""" -row = '''
+row = """ -''' +""" -footer = ''' - ''' + """ diff --git a/phigaro/to_html/preprocess.py b/phigaro/to_html/preprocess.py index 7f1464c..937c55a 100644 --- a/phigaro/to_html/preprocess.py +++ b/phigaro/to_html/preprocess.py @@ -1,4 +1,4 @@ -import pickle +import pandas as pd import plotly.graph_objs as go from plotly.offline import plot import numpy as np @@ -6,17 +6,17 @@ from Bio import SeqIO pvogs_groups = [ - 'Lysis', - 'Integration', - 'Terminase', - 'Replication', - 'Coat', - 'Baseplate', - 'Tail', - 'Assembly', - 'Portal', - 'Other (structural)', - 'Other', + "Lysis", + "Integration", + "Terminase", + "Replication", + "Coat", + "Baseplate", + "Tail", + "Assembly", + "Portal", + "Other (structural)", + "Other", ] cmap = [ (31, 119, 180), @@ -33,21 +33,19 @@ ] colors = {group: cmap[i] for i, group in enumerate(pvogs_groups)} -with open( - os.path.dirname(os.path.abspath(__file__)) + '/pvogs_annotations.pickle', - 'rb', -) as f: - annotations = pickle.load(f) +annotations = pd.read_csv( + os.path.dirname(os.path.abspath(__file__)) + "/pvogs_annotations.csv", index_col=0 +) def form_arrow(begin, end, nonreverse, width): - ''' + """ :param begin: int (of gene) :param end: int (of gene) :param nonreverse: boolean :param width: :return: tuple of tuples (arrow coords) - ''' + """ k = 0.05 height = 0.9 if width < 0.4 else 1 width = width if width > 0.6 else 0.6 @@ -74,10 +72,10 @@ def form_arrow(begin, end, nonreverse, width): def plot_html(records, prophage_begin, prophage_end): - ''' + """ :param records: list of Gene :return: html_plot - ''' + """ def _plotly_to_html_( prophage_begin, prophage_end, func_groups, widths, coords, arrow_coords @@ -87,12 +85,12 @@ def _plotly_to_html_( go.Scatter( x=[prophage_begin], y=[100], - mode='markers', + mode="markers", opacity=1, - hoverinfo='none', + hoverinfo="none", marker=dict( size=10, - color='rgba(%.5f, %.5f, %.5f, 0.8)' % colors[group], + color="rgba(%.5f, %.5f, %.5f, 0.8)" % colors[group], ), name=group, ) @@ -103,11 +101,11 @@ def _plotly_to_html_( x=np.array(coords)[elements], y=[1] * len(elements), text=np.array(records_info)[elements], - hoverinfo='text', - mode='markers', + hoverinfo="text", + mode="markers", marker=dict( size=90 * np.array(widths)[elements], - color='rgba(%.5f, %.5f, %.5f, 1)' % colors[group], + color="rgba(%.5f, %.5f, %.5f, 1)" % colors[group], opacity=0, ), showlegend=False, @@ -118,39 +116,39 @@ def _plotly_to_html_( go.Scatter( x=[prophage_begin, prophage_end], y=[1, 1], - mode='lines', - line=dict(color='rgba(116,116,116, 0.5)', width=1), - hoverinfo='none', + mode="lines", + line=dict(color="rgba(116,116,116, 0.5)", width=1), + hoverinfo="none", showlegend=False, ) ] layout = { - 'template':'plotly_white', - 'yaxis': dict( + "template": "plotly_white", + "yaxis": dict( range=[-0.5, 2.5], showgrid=False, zeroline=False, showline=False, - ticks='', + ticks="", showticklabels=False, ), - 'xaxis': dict(title='Nucleotide Number'), - 'shapes': [ + "xaxis": dict(title="Nucleotide Number"), + "shapes": [ { - 'type': 'path', - 'path': 'M ' - + ' '.join( + "type": "path", + "path": "M " + + " ".join( [ - 'L {:.5f},{:.5f}'.format(*arrow_point) + "L {:.5f},{:.5f}".format(*arrow_point) for arrow_point in arrow ] )[1:] - + ' Z', - 'fillcolor': 'rgba(%.5f, %.5f, %.5f, 1)' + + " Z", + "fillcolor": "rgba(%.5f, %.5f, %.5f, 1)" % colors[group], # 'rgba(44, 160, 101, 0.5)' - 'opacity': 0.7, - 'line': { - 'color': 'rgba(%.5f, %.5f, %.5f, 0.7)' % colors[group], + "opacity": 0.7, + "line": { + "color": "rgba(%.5f, %.5f, %.5f, 0.7)" % colors[group], }, } for group, elements in func_groups.items() @@ -159,8 +157,8 @@ def _plotly_to_html_( } data = traces0 + trace1 fig = { - 'data': data, - 'layout': layout, + "data": data, + "layout": layout, } return fig @@ -176,47 +174,44 @@ def _plotly_to_html_( coords.append(record.begin + (record.end - record.begin) / 2.0) arrow_coords.append((record.begin, record.end, (record.strand + 1) / 2)) records_info.append( - '%s
%d-%d
gc_cont = %s' + "%s
%d-%d
gc_cont = %s" % (record.vog_name, record.begin, record.end, record.gc_cont) ) group = ( annotations.loc[record.vog_name.strip()].group if record.vog_name.strip() in annotations.index - else 'Other' + else "Other" ) if group in func_groups.keys(): func_groups[group].append(i) else: func_groups[group] = [i] if len(widths) > 0: - widths = 1.0 * (np.array(widths) - min(widths)) / max(widths) + 0.1 - arrow_coords = [ - form_arrow(*info, width=width) - for info, width in zip(arrow_coords, widths) - ] + widths = 1.0 * (np.array(widths) - min(widths)) / max(widths) + 0.1 + arrow_coords = [ + form_arrow(*info, width=width) for info, width in zip(arrow_coords, widths) + ] plotly_fig = _plotly_to_html_( prophage_begin, prophage_end, func_groups, widths, coords, arrow_coords ) return plot( plotly_fig, include_plotlyjs=False, - filename='gene_map.html', - output_type='div', + filename="gene_map.html", + output_type="div", ) -def form_sequence( - fasta_file, fasta_name, prophage_begin, prophage_end, scaffold_name -): +def form_sequence(fasta_file, fasta_name, prophage_begin, prophage_end, scaffold_name): for record in SeqIO.parse(fasta_file, "fasta"): if record.id.strip() == scaffold_name.strip(): sequence = record.seq[prophage_begin : (prophage_end + 1)] clean_sequence = sequence ins_ind = 77 while ins_ind < len(sequence): - sequence = sequence[:ins_ind] + '%0A' + sequence[ins_ind:] + sequence = sequence[:ins_ind] + "%0A" + sequence[ins_ind:] ins_ind += 80 - sequence = '%' + '3E%s' % fasta_name + '%' + '0A%s' % sequence + sequence = "%" + "3E%s" % fasta_name + "%" + "0A%s" % sequence return sequence, clean_sequence @@ -226,12 +221,12 @@ def if_transposable(records): group = ( annotations.loc[record.vog_name.strip()].group if record.vog_name.strip() in annotations.index - else 'Other' + else "Other" ) - if (group == 'Integration') & status: + if (group == "Integration") & status: return True - elif group == 'Integration': + elif group == "Integration": status = True - elif (group != 'Integration') & (group != 'Other'): + elif (group != "Integration") & (group != "Other"): status = False return False diff --git a/phigaro/to_html/pvogs_annotations.csv b/phigaro/to_html/pvogs_annotations.csv new file mode 100644 index 0000000..bd449a2 --- /dev/null +++ b/phigaro/to_html/pvogs_annotations.csv @@ -0,0 +1,1475 @@ +,function,group +VOG0001,V protein,Other +VOG0002,major coat protein,Coat +VOG0005,phage assembly protein,Assembly +VOG0006,Vpf491,Other +VOG0007,putative minor coat protein,Coat +VOG0009,putative transcription regulator,Other +VOG0013,DNA replication initiation protein,Replication +VOG0015,putative major coat protein,Coat +VOG0016,S-adenosyl-L-methionine hydrolase,Other +VOG0018,DNA ligase,Replication +VOG0019,RNA polymerase,Other +VOG0025,putative DNA helicase,Replication +VOG0026,DNA polymerase,Replication +VOG0028,exonuclease,Other +VOG0030,head-tail connector protein,Other (structural) +VOG0031,capsid assembly protein,Assembly +VOG0034,tail tubular protein B,Tail +VOG0035,internal virion protein A,Other +VOG0037,internal virion protein C,Other +VOG0038,internal virion protein D,Other +VOG0040,type II holin,Lysis +VOG0046,superinfection exclusion protein,Other +VOG0049,RtcB,Other +VOG0050,dCMP deaminase,Other +VOG0051,terminase large subunit,Terminase +VOG0052,RNA polymerase sigma factor,Other +VOG0054,holin,Lysis +VOG0058,P-starvation inducible protein,Other +VOG0061,major capsid protein,Coat +VOG0067,tail sheath protein,Tail +VOG0083,recombination endonuclease subunit,Other +VOG0085,deoxyuridine 5'-triphosphate nucleotidohydrolase,Other +VOG0088,ribonucleotide reductase,Other +VOG0092,thymidylate synthase,Other +VOG0106,terminase large subunit,Terminase +VOG0136,holin,Lysis +VOG0156,serine/threonine protein phosphatase,Other +VOG0166,maturation protein,Assembly +VOG0167,replicase,Replication +VOG0168,gpA,Other +VOG0169,gpA*,Other +VOG0170,gpB,Other +VOG0171,gpK,Other +VOG0172,gpC,Other +VOG0173,gpD,Other +VOG0174,gpE,Other +VOG0175,gpJ,Other +VOG0176,gpF,Other +VOG0177,gpG,Other +VOG0178,gpH,Other +VOG0183,putative transcription regulator,Other +VOG0189,DNA replication protein,Replication +VOG0202,putative head-tail joining protein,Other (structural) +VOG0205,putative head-tail joining protein,Other (structural) +VOG0209,putative tail component protein,Tail +VOG0221,integrase,Integration +VOG0227,tail fiber assembly protein,Assembly +VOG0234,ParB,Other +VOG0236,Gp63,Other +VOG0237,LysC,Other +VOG0249,Doc,Other +VOG0253,terminase small subunit,Terminase +VOG0254,portal protein,Portal +VOG0258,DNA stabilization protein,Other +VOG0259,DNA stabilization protein,Other +VOG0261,head assembly protein,Assembly +VOG0263,DNA transfer protein,Other +VOG0265,DNA transfer protein,Other +VOG0273,O-antigen conversion protein C,Other +VOG0274,GtrB,Other +VOG0275,integrase,Integration +VOG0281,Abc2 protein,Other +VOG0284,Arf,Other +VOG0285,Kil,Other +VOG0286,CIII protein,Other +VOG0287,SieB,Other +VOG0288,antitermination protein N,Other +VOG0292,NinB protein,Other +VOG0293,NinE protein,Other +VOG0295,NinF protein,Other +VOG0296,NinG protein,Other +VOG0298,late gene regulator Q,Other +VOG0299,endopeptidase,Other +VOG0300,Rz1 protein,Other +VOG0312,Gp18 protein,Other +VOG0320,Gp45 protein,Other +VOG0334,DNA polymerase,Replication +VOG0337,putative DNA-packaging protein,Other +VOG0350,nicotinamide phosphoribosyltransferase,Other +VOG0351,prohead core scaffolding protein and protease,Other +VOG0355,replication protein P,Replication +VOG0356,tail sheath protein,Tail +VOG0372,NAD-dependent DNA ligase subunit A,Replication +VOG0377,DNA helicase,Replication +VOG0382,DNA topoisomerase II large subunit,Replication +VOG0384,DNA topisomerase II medium subunit,Other +VOG0393,ADP-ribosylase,Other +VOG0397,dUTPase,Other +VOG0400,spackle periplasmic protein,Other +VOG0402,head vertex assembly chaperone,Assembly +VOG0408,clamp loader subunit,Other +VOG0409,sliding clamp DNA polymerase accessory protein,Replication +VOG0410,RNA polymerase binding protein,Other +VOG0412,alpha-glucosyl-transferase,Other +VOG0419,anaerobic NTP reductase small subunit,Other +VOG0420,anaerobic NTP reductase large subunit,Other +VOG0421,inhibitor of host Lon protease,Other +VOG0436,site-specific RNA endonuclease,Other +VOG0443,nudix hydrolase,Other +VOG0451,head completion protein,Assembly +VOG0452,baseplate wedge subunit,Baseplate +VOG0454,baseplate wedge subunit,Baseplate +VOG0456,baseplate wedge subunit and tail pin,Tail +VOG0457,baseplate wedge subunit and tail pin,Tail +VOG0459,fibritin,Other +VOG0460,neck protein,Other +VOG0461,neck protein,Other +VOG0462,tail sheath stabilizer and completion protein,Assembly +VOG0463,prohead core protein,Other +VOG0464,prohead core protein,Other +VOG0465,scaffold prohead core protein,Other +VOG0466,major capsid protein,Coat +VOG0471,inhibitor of prohead protease,Other +VOG0473,UvsY,Other +VOG0474,baseplate hub subunit,Baseplate +VOG0475,baseplate hub distal subunit,Baseplate +VOG0476,baseplate hub subunit tail length determinator,Tail +VOG0477,baseplate tail tube cap,Tail +VOG0480,ADP-ribosyltransferase,Other +VOG0485,lysis inhibition accessory protein,Other +VOG0493,endonuclease II,Other +VOG0496,dihydrofolate reductase,Other +VOG0499,single-stranded DNA binding protein,Other +VOG0505,holin lysis mediator,Lysis +VOG0509,activator of middle period transcription,Other +VOG0510,nucleoid disruption protein,Other +VOG0529,Na/K ATPase,Other +VOG0544,Panton-Valentine leukocidin chain S precursor,Other +VOG0545,Panton-Valentine leukocidin chain F precursor,Other +VOG0559,transcriptional activator RinB,Other +VOG0566,capsid-scaffolding protein,Other +VOG0567,terminase endonuclease subunit,Terminase +VOG0568,head completion-stabilization protein,Assembly +VOG0569,tail synthesis protein X,Tail +VOG0571,tail protein,Tail +VOG0574,tail formation protein I,Assembly +VOG0577,major tail tube protein,Tail +VOG0582,tail protein,Tail +VOG0588,replication protein A,Replication +VOG0602,holin,Lysis +VOG0603,gpJ,Other +VOG0609,scaffolding protein,Other +VOG0612,terminase small subunit,Terminase +VOG0614,lysin,Lysis +VOG0615,holin,Lysis +VOG0639,DNA encapsidation protein,Assembly +VOG0641,holin,Lysis +VOG0642,lower collar protein,Other +VOG0643,major head protein,Other +VOG0644,upper collar protein,Other +VOG0645,tail protein,Tail +VOG0647,putative minor structural protein,Other +VOG0668,putative DNA polymerase I,Replication +VOG0676,RNA ligase,Other +VOG0681,gpK,Other +VOG0691,portal protein,Portal +VOG0692,minor capsid protein,Coat +VOG0694,major capsid protein,Coat +VOG0697,putative minor capsid protein,Coat +VOG0698,putative minor capsid protein,Coat +VOG0703,holin,Lysis +VOG0705,FtsK/SpoIIIE protein,Other +VOG0707,conserved phage protein,Other +VOG0720,portal protein,Portal +VOG0731,holin,Lysis +VOG0739,putative topoisomerase,Replication +VOG0756,Rad52/22 family double-strand break repair protein,Other +VOG0764,capsid protein,Coat +VOG0765,holin,Lysis +VOG0785,excisionase,Other +VOG0796,terminase small subunit,Terminase +VOG0799,major tail protein,Tail +VOG0816,head-tail adaptor,Other +VOG0823,excisionase,Other +VOG0827,mobile element protein,Other +VOG0828,putative single-stranded DNA binding protein,Other +VOG0830,Bor protein precursor,Other +VOG0831,terminase small subunit nu1,Terminase +VOG0832,head-to-tail joining protein,Other (structural) +VOG0833,portal protein,Portal +VOG0835,head-DNA stabilization protein,Other +VOG0837,DNA packaging protein,Other +VOG0838,head-tail connector Fii,Other (structural) +VOG0839,minor tail protein,Tail +VOG0840,minor tail protein U,Tail +VOG0842,minor tail protein G,Tail +VOG0843,minor tail protein,Tail +VOG0847,minor tail protein,Tail +VOG0848,minor tail protein,Tail +VOG0850,tail protein,Tail +VOG0855,attachment invasion locus protein precursor,Other +VOG0875,terminal protein,Other +VOG0876,transcriptional regulator,Other +VOG0877,single stranded DNA-binding protein,Other +VOG0878,dsDNA binding protein,Other +VOG0879,scaffolding protein,Other +VOG0880,head fiber protein,Other +VOG0885,DNA replication organizer,Replication +VOG0886,putative protein 16.8,Other +VOG0887,putative terminase small subunit,Terminase +VOG0889,putative strucural protein 2,Other +VOG0890,putative strucural protein 4,Other +VOG0897,holin,Lysis +VOG0906,putative sak protein,Other +VOG0913,putative structural protein,Other +VOG0924,putative DNA polymerase subunit,Replication +VOG0930,putative strucural protein 3,Other +VOG0933,neck passage structure,Other +VOG0944,transposase,Integration +VOG0945,mobile element protein,Other +VOG0946,shiga-like toxin II subunit A precursor,Other +VOG0947,Shiga toxin 2 subunit B,Other +VOG0975,Putative small subunit (Nu1 homolog) of DNA packaging dimer,Other +VOG0976,major capsid protein,Coat +VOG0979,retron-type RNA-directed DNA polymerase,Other +VOG0985,ParA,Other +VOG0986,protelomerase,Other +VOG0991,gp55 protein,Other +VOG0992,putative endolysin,Lysis +VOG0996,clamp loader subunit,Other +VOG0997,baseplate hub subunit,Baseplate +VOG0998,queuosine biosynthesis QueE radical SAM,Other +VOG1001,portal vertex protein,Portal +VOG1005,tail tube protein,Tail +VOG1006,sigma factor for late transcription,Other +VOG1020,QueC,Other +VOG1026,transposase,Integration +VOG1030,thymidine kinase,Other +VOG1031,nucleotide-sugar epimerase,Other +VOG1032,gp4,Other +VOG1036,putative co-chaperonin GroES,Other +VOG1045,putative HTH transcription regulator,Other +VOG1051,UDP-galactopyranose mutase,Other +VOG1072,EPS-depolymerase,Replication +VOG1092,terminase small subunit,Terminase +VOG1099,major capsid protein,Coat +VOG1105,major tail subunit,Tail +VOG1112,minor tail protein,Tail +VOG1113,minor tail protein,Tail +VOG1146,RNaseE,Other +VOG1165,minor tail protein,Tail +VOG1166,minor tail protein,Tail +VOG1167,minor tail protein,Tail +VOG1179,gp81,Other +VOG1184,gp40,Other +VOG1190,portal protein,Portal +VOG1191,major capsid protein,Coat +VOG1198,DNA polymerase III alpha subunit,Replication +VOG1200,galactosyltransferase,Other +VOG1201,glycosyltransferase,Other +VOG1213,tail assembly chaperone,Assembly +VOG1215,minor tail protein,Tail +VOG1222,holin,Lysis +VOG1225,Lsr2,Other +VOG1270,gp13,Other +VOG1279,predicted hydrolase,Other +VOG1284,CHC2 zinc finger protein,Other +VOG1297,conserved hypothetical protein,Other +VOG1298,putative methyltransferase,Other +VOG1300,conserved hypothetical protein,Other +VOG1309,RecT,Other +VOG1311,PcfU,Other +VOG1314,conserved hypothetical protein,Other +VOG1319,major head protein,Other +VOG1329,major capsid protein,Coat +VOG1337,HNH endonuclease,Other +VOG1344,nicotinamide mononucleotide transporter,Other +VOG1363,putative Sir2-like protein,Other +VOG1391,transaldolase-like protein,Other +VOG1403,DUF680 domain-containing protein,Other +VOG1404,photosystem II D1 protein,Other +VOG1405,high light inducible protein,Other +VOG1436,tail fiber protein,Tail +VOG1517,putative terminase small subunit,Terminase +VOG1519,putative tail protein,Tail +VOG1587,tail assembly chaperone,Assembly +VOG1590,minor tail protein,Tail +VOG1609,DNA primase,Replication +VOG1617,gp63,Other +VOG1618,gp80,Other +VOG1619,gp75,Other +VOG1647,ParB,Other +VOG1654,esterase/lipase,Other +VOG1681,translation repressor,Other +VOG1801,base plate hub assembly catalyst,Assembly +VOG1829,head assembly cochaperone with GroEL,Assembly +VOG1850,tRNA nucleotidyltransferase,Other +VOG1860,loader of DNA helicase,Replication +VOG1861,late promoter transcription accessory protein,Other +VOG1864,anti-sigma 70 protein,Other +VOG1871,NudE nudix hydrolase,Other +VOG1874,gp35 hinge long tail fiber proximal connector,Other (structural) +VOG1883,gp13,Other +VOG1886,putative terminase large subunit,Terminase +VOG1887,major capsid protein,Coat +VOG1894,holin,Lysis +VOG1898,cell adhesion domain-containing protein,Other +VOG1912,putative portal protein,Portal +VOG1936,AAA ATPase,Other +VOG1981,small outer capsid protein,Coat +VOG1992,internal head protein,Other +VOG2005,homing endonuclease,Other +VOG2006,hinge connector of long tail fiber proximal connector,Other (structural) +VOG2012,DNA endonuclease IV,Other +VOG2015,gp5,Other +VOG2017,gp8,Other +VOG2044,gp3,Other +VOG2054,phosphoribosyl transferase,Other +VOG2075,terminase small subunit,Terminase +VOG2080,Cor protein,Other +VOG2090,serine/threonine kinase,Other +VOG2098,DNA packaging protein,Other +VOG2120,putative major tail protein,Tail +VOG2123,methyltransferase,Other +VOG2124,Ren protein,Other +VOG2137,major tropism determinant,Other +VOG2142,transposase A,Integration +VOG2200,acridine resistance protein,Other +VOG2210,putative tail tube protein,Tail +VOG2211,putative tail sheath protein,Tail +VOG2215,CI,Other +VOG2217,holin,Lysis +VOG2218,Apl,Other +VOG2232,minor capsid protein,Coat +VOG2233,replication protein VP4,Replication +VOG2234,major capsid protein VP1,Coat +VOG2235,internal scaffolding protein VP3,Other +VOG2310,protein kinase,Other +VOG2312,host dGTPase inhibitor,Other +VOG2313,gp1.5,Other +VOG2315,host RNA polymerase inhibitor,Other +VOG2332,HNH endonuclease,Other +VOG2352,guanylate kinase,Other +VOG2368,"ribonucleoside triphosphate reductase, alpha chain",Other +VOG2379,virion RNA polymerase,Other +VOG2384,major coat protein,Coat +VOG2386,portal protein,Portal +VOG2397,single stranded DNA-binding protein,Other +VOG2403,phage lambda Rz1-like protein,Other +VOG2422,valyl-tRNA synthetase modifier,Other +VOG2444,transcription modulator,Other +VOG2450,distal long tail fiber assembly catalyst,Assembly +VOG2457,IpI,Other +VOG2497,gp3,Other +VOG2513,tail assembly chaperone,Assembly +VOG2518,minor tail protein,Tail +VOG2526,holin,Lysis +VOG2557,antirestriction protein,Other +VOG2559,gp1,Other +VOG2560,terminase small subunit,Terminase +VOG2567,tail assembly chaperone,Assembly +VOG2570,gp28,Other +VOG2571,gp31,Other +VOG2575,metallophosphoesterase,Other +VOG2612,gp2,Other +VOG2613,gp9,Other +VOG2617,gp16,Other +VOG2621,gp24,Other +VOG2622,tail assembly chaperone,Assembly +VOG2624,gp28,Other +VOG2626,gp33,Other +VOG2627,gp34,Other +VOG2634,gp1,Other +VOG2636,gp59,Other +VOG2637,gp2,Other +VOG2644,holin,Lysis +VOG2648,HTH DNA binding protein,Other +VOG2649,GIY-YIG endonuclease,Other +VOG2654,HTH DNA binding protein,Other +VOG2666,gp96,Other +VOG2766,putative holin,Lysis +VOG2773,putative transcriptional regulator,Other +VOG2774,putative DNA primase,Replication +VOG2786,Ner-like protein,Other +VOG2788,DNA transposition protein,Other +VOG2791,tail sheath protein,Tail +VOG2792,tail/DNA circulation protein,Tail +VOG2793,tail protein,Tail +VOG2806,putative head protein,Other +VOG2819,Ser/Thr kinase,Other +VOG2820,glycosyltransferase,Other +VOG2821,gp18,Other +VOG2822,gp21,Other +VOG2842,LipC,Other +VOG2848,AddA-like protein,Other +VOG2875,gp205,Other +VOG2876,Ku protein,Other +VOG2894,gp4,Other +VOG2895,gp7,Other +VOG2914,gp78,Other +VOG2920,gp56,Other +VOG2922,RDF protein,Other +VOG2923,gp82,Other +VOG2924,gp85,Other +VOG2925,gp86,Other +VOG2932,terminase small subunit,Terminase +VOG2933,enoyl-CoA-hydratase,Other +VOG2936,methyltransferase,Other +VOG2937,gp19,Other +VOG2947,gp91,Other +VOG2950,gp94,Other +VOG2957,gp148,Other +VOG2958,gp131,Other +VOG2973,gp205,Other +VOG2993,gp5,Other +VOG2995,phosphoesterase,Other +VOG3011,tyrosine phosphatase,Other +VOG3015,gp37,Other +VOG3020,gp4,Other +VOG3022,gp67,Other +VOG3028,gp1,Other +VOG3029,gp3,Other +VOG3030,gp139,Other +VOG3050,RecA,Other +VOG3093,ATP-dependent helicase,Replication +VOG3178,major capsid protein,Coat +VOG3180,maturation/adhesion protein,Assembly +VOG3181,gp82,Other +VOG3188,gp18,Other +VOG3199,gp22,Other +VOG3201,gp29,Other +VOG3202,gp30,Other +VOG3211,gp15,Other +VOG3215,FtsK-like protein,Other +VOG3221,gp90,Other +VOG3222,GTP cyclohydrolase I,Other +VOG3227,putative tail fiber,Tail +VOG3233,phosphatidylglycerophosphatase A,Other +VOG3235,IMP dehydrogenase/GMP reductase,Other +VOG3238,small acid-soluble spore protein,Other +VOG3239,putative DNA helicase,Replication +VOG3241,Ser/Thr protein phosphatase family protein,Other +VOG3244,putative UV damage repair endonuclease,Other +VOG3255,virion structural protein,Other +VOG3256,virion structural protein,Other +VOG3262,putative helicase,Replication +VOG3263,major capsid protein,Coat +VOG3271,virion structural protein,Other +VOG3275,virion structural protein,Other +VOG3278,putative tail sheath protein,Tail +VOG3279,putative virion structural protein,Other +VOG3280,putative virion structural protein,Other +VOG3287,"addiction module toxin, RelE/StbE family",Other +VOG3288,Vpf76,Other +VOG3294,activator of host PrrC lysyl-tRNA endonuclease,Other +VOG3309,putative excisionase,Other +VOG3341,minor coat protein,Coat +VOG3344,integrase,Integration +VOG3346,putative HTH transcriptional regulator,Other +VOG3347,helix-turn-helix protein,Other +VOG3356,structural protein V1,Other +VOG3357,structural protein VP3,Other +VOG3358,VP2-like protein,Other +VOG3369,NinD,Other +VOG3376,host recBCD nuclease inhibitor,Other +VOG3379,Cox,Other +VOG3381,Hol,Other +VOG3382,nonstructural protein,Other +VOG3396,Gp29,Other +VOG3397,gp33,Other +VOG3399,gp42 protein,Other +VOG3401,transcription antiterminator,Other +VOG3404,gp51,Other +VOG3416,minor tail protein,Tail +VOG3418,gp3,Other +VOG3419,gp4a,Other +VOG3420,gp5,Other +VOG3421,gp12,Other +VOG3427,major tail subunit,Tail +VOG3443,GtrA,Other +VOG3445,NinY,Other +VOG3447,O-polysaccharide acetyltransferase protein,Other +VOG3475,putative transcription regulator,Other +VOG3478,excisionase,Other +VOG3505,CRISPR-associated Cas4-like protein,Other +VOG3506,putative helicase,Replication +VOG3518,DNA binding protein,Other +VOG3519,putative regulatory protein,Other +VOG3520,putative regulatory protein,Other +VOG3525,structural protein,Other +VOG3526,structural protein,Other +VOG3530,putative glycosyltransferase,Other +VOG3546,gp32,Other +VOG3550,gp40,Other +VOG3552,gp46,Other +VOG3562,exfoliative toxin A,Other +VOG3563,"gp8, conserved hypothetical protein",Other +VOG3564,gp71,Other +VOG3567,gp17,Other +VOG3570,"gp26, bacteriophage lysis protein",Lysis +VOG3571,gp27,Other +VOG3574,gp29,Other +VOG3576,gp30,Other +VOG3577,gp31,Other +VOG3578,"gp32, hypothetical protein",Other +VOG3583,"gp45, hypothetical protein",Other +VOG3585,gp63,Other +VOG3586,putative chromosome partitioning protein,Other +VOG3588,gp62,Other +VOG3590,gp4,Other +VOG3591,gp65,Other +VOG3593,"gp43, conserved domain protein",Other +VOG3607,putative integral membrane protein,Other +VOG3624,putative transposase,Integration +VOG3653,tail protein,Tail +VOG3654,putative protease,Other +VOG3660,gp19,Other +VOG3667,BcepNY3gp56,Other +VOG3669,gp62,Other +VOG3675,scaffolding protein,Other +VOG3676,major head protein,Other +VOG3704,excisionase,Other +VOG3708,77ORF046,Other +VOG3721,virion structural protein,Other +VOG3722,thymidylate kinase,Other +VOG3724,putative SNF2 domain helicase,Replication +VOG3739,putative endoprotease,Other +VOG3740,major capsid protein,Coat +VOG3744,Rz1 gp24',Other +VOG3760,p11,Other +VOG3777,p53,Other +VOG3793,putative internal virion protein A,Other +VOG3824,DNA polymerase,Replication +VOG3843,putative glutathionylspermidine synthase,Other +VOG3887,"gp40, hypothetical protein",Other +VOG3890,putative tail sheath protein,Tail +VOG3897,gp2,Other +VOG3900,gp63,Other +VOG3921,A2 protein,Other +VOG3967,D2 protein,Other +VOG3969,D3 protein,Other +VOG3972,D5 protein,Other +VOG3978,tail protein Pb4,Tail +VOG3979,tail protein,Tail +VOG3981,pore-forming tail tip protein,Tail +VOG3984,minor tail protein,Tail +VOG3995,putative transposase A subunit,Integration +VOG4006,gp35,Other +VOG4017,2OG-Fe(II) oxygenase,Other +VOG4023,structural protein,Other +VOG4026,virion structural protein,Other +VOG4027,tail fiber-like protein,Tail +VOG4037,methylamine protein,Other +VOG4040,peptidase,Other +VOG4044,heat shock protein,Other +VOG4059,virion structural protein,Other +VOG4062,photosystem II D2 protein,Other +VOG4070,S-adenosylmethionine decarboxylase,Other +VOG4079,antenna protein,Other +VOG4080,2OG-Fe(II) oxygenase,Other +VOG4085,ferrochelatase,Other +VOG4088,tryptophan halogenase,Other +VOG4097,phycoerythrobilin,Other +VOG4099,CP12 protein,Other +VOG4111,baseplate wedge initiator,Baseplate +VOG4120,DNA endonuclease V,Other +VOG4123,5-phosphoribosylformylglycinamide amidotransferase,Other +VOG4124,phosphoribosylaminoimidazole synthetase,Other +VOG4125,phosphoribosylaminoimidazole synthetase,Other +VOG4126,cytitidyltransferase,Other +VOG4128,plasmid stability protein,Other +VOG4133,plastocyanine,Other +VOG4138,phosphate transporter subunit,Other +VOG4142,glycosyltransferase family 11,Other +VOG4143,glycosyltransferase family 25,Other +VOG4149,ferredoxin,Other +VOG4152,heme oxygenase,Other +VOG4154,carbamoyltransferase,Other +VOG4155,putative nucleotidyltransferase,Other +VOG4156,putative carbohydrate kinase,Other +VOG4157,putative nucleotidyltransferase,Other +VOG4161,cAMP phosphodiesterase,Other +VOG4165,structural protein,Other +VOG4166,putative short tail fiber,Tail +VOG4191,hemagglutinin domain-containing protein,Other +VOG4192,structural protein,Other +VOG4195,plastoquinol terminal oxidase,Other +VOG4204,S-layer domain protein,Other +VOG4210,carboxylesterase,Other +VOG4319,putative major capsid protein,Coat +VOG4341,gp2,Other +VOG4344,putative membrane protein,Other +VOG4357,transposase,Integration +VOG4359,putative transposase,Integration +VOG4409,6-phosphogluconate dehydrogenase,Other +VOG4410,glucose 6-phosphate dehydrogenase,Other +VOG4418,DUF1583 domain-containing protein,Other +VOG4447,putative phosphatase,Other +VOG4495,putative bacterial NUDIX hydrolase,Other +VOG4524,phosphoribosylaminoimidazole-succinocarboxamide synthase,Other +VOG4536,PA14 domain-containing protein,Other +VOG4542,RNA-dependent RNA polymerase,Other +VOG4544,terminase large subunit,Terminase +VOG4545,tape measure protein,Other +VOG4547,lysin A,Lysis +VOG4548,helicase,Replication +VOG4549,glutaredoxin,Other +VOG4551,DNA primase,Replication +VOG4553,major capsid protein,Coat +VOG4555,scaffolding protein,Other +VOG4556,portal protein,Portal +VOG4557,major tail subunit,Tail +VOG4558,minor tail protein,Tail +VOG4560,lysin B,Lysis +VOG4561,thymidylate synthase,Other +VOG4562,ribonucleotide reductase subunit B,Other +VOG4565,lysozyme,Other +VOG4567,DNA methylase,Other +VOG4569,minor tail protein,Tail +VOG4571,DNA methylase,Other +VOG4572,major capsid protein,Coat +VOG4574,lysin A,Lysis +VOG4575,recombination endonuclease subunit,Other +VOG4577,DNA polymerase,Replication +VOG4582,tail assembly chaperone,Assembly +VOG4583,WhiB,Other +VOG4584,baseplate hub subunit and tail lysozyme,Tail +VOG4586,major tail protein,Tail +VOG4588,D-ala-D-ala carboxypeptidase,Other +VOG4591,baseplate wedge tail fiber connector,Other (structural) +VOG4592,tail tubular protein A,Tail +VOG4594,protector from prophage-induced early lysis,Other +VOG4595,DNA end protector protein,Other +VOG4598,tail fiber protein,Tail +VOG4599,minor structural protein,Other +VOG4600,exonuclease,Other +VOG4601,major capsid protein,Coat +VOG4603,gp46,Other +VOG4604,portal protein,Portal +VOG4606,DNA primase,Replication +VOG4608,replicative helicase,Replication +VOG4610,internal virion protein B,Other +VOG4613,putative tail lysin,Lysis +VOG4618,gp1,Other +VOG4625,hinge connector of long tail fiber distal connector,Other (structural) +VOG4627,glycosyltransferase,Other +VOG4630,tail protein,Tail +VOG4634,major tail subunit,Tail +VOG4637,tail assembly chaperone,Assembly +VOG4640,tailspike protein,Tail +VOG4641,capsid maturation protease,Assembly +VOG4644,baseplate J,Baseplate +VOG4645,LysB,Other +VOG4646,putative tail fiber protein,Tail +VOG4648,putative helicase-primase,Replication +VOG4649,lysin,Lysis +VOG4650,integrase,Integration +VOG4652,virion morphogenesis protein,Other +VOG4653,baseplate hub subunit and tail lysozyme,Tail +VOG4658,DNA methylase,Other +VOG4659,putative antireceptor,Other +VOG4660,pre-neck appendage protein,Other +VOG4661,putative replication origin binding protein,Replication +VOG4663,gp29,Other +VOG4666,lysin A,Lysis +VOG4668,assembly protein,Assembly +VOG4669,tailspike 63D sialidase,Tail +VOG4672,head maturation protease,Assembly +VOG4673,conserved phage protein,Other +VOG4676,WhiB,Other +VOG4677,putative poly A polymerase,Replication +VOG4678,glycosyltransferase/methyl transferase,Other +VOG4681,gp22,Other +VOG4683,structural protein,Other +VOG4686,morphogenesis protein,Other +VOG4689,gp54,Other +VOG4690,transcriptional regulator,Other +VOG4692,exonuclease,Other +VOG4695,baseplate wedge subunit,Baseplate +VOG4696,terminase small subunit,Terminase +VOG4697,tail completion and sheath stabilizer protein,Assembly +VOG4698,RNA ligase,Other +VOG4701,tail assembly protein,Assembly +VOG4702,baseplate wedge subunit,Baseplate +VOG4707,putative endolysin,Lysis +VOG4708,RecE,Other +VOG4711,major capsid protein,Coat +VOG4712,inhibitor of host transcription,Other +VOG4714,ribonuclease H,Other +VOG4715,baseplate wedge protein,Baseplate +VOG4719,modifier of suppressor tRNAs,Other +VOG4725,gp6,Other +VOG4730,flavodoxin,Other +VOG4733,DNA methylase,Other +VOG4735,tail protein,Tail +VOG4736,tail protein,Tail +VOG4745,Kil protein,Other +VOG4759,glycosyl transferase,Other +VOG4760,minor tail protein,Tail +VOG4761,minor tail protein,Tail +VOG4763,peptidase_S74 domain protein,Other +VOG4771,terminase small subunit,Terminase +VOG4772,N-acetylmuramoyl-L-alanine amidase,Other +VOG4773,capsid portal protein Q,Portal +VOG4774,gp11,Other +VOG4777,histidine triad domain protein,Other +VOG4779,DNA delivery,Other +VOG4781,putative tail protein,Tail +VOG4790,major tail protein,Tail +VOG4795,endolysin,Lysis +VOG4802,O-methyltransferase,Other +VOG4806,putative ribonuclease H,Other +VOG4809,NAD-dependent DNA ligase,Replication +VOG4810,modifier of transcription,Other +VOG4811,tapemeasure,Other +VOG4814,DNA packaging ATPase,Other +VOG4815,gp74,Other +VOG4820,tail protein,Tail +VOG4823,Hoc large outer capsid protein,Coat +VOG4825,homing endonuclease,Other +VOG4827,putative baseplate wedge protein,Baseplate +VOG4832,long tail fiber distal subunit,Tail +VOG4835,gp142,Other +VOG4837,gp31,Other +VOG4838,WhiB,Other +VOG4840,gp13,Other +VOG4844,putative terminase small subunit,Terminase +VOG4850,lysin,Lysis +VOG4854,putative excisionase,Other +VOG4855,recombinase,Other +VOG4860,internal (core) protein,Other +VOG4865,LysM domain-containing protein,Other +VOG4868,tailspike,Tail +VOG4882,DR0530-like primase,Replication +VOG4884,distal tail protein,Tail +VOG4885,late control D protein,Other +VOG4909,tail protein,Tail +VOG4910,putative peptidase M23,Other +VOG4934,putative holin,Lysis +VOG4942,Uncharacterized protein MJ0770,Other +VOG4952,ATPase family protein,Other +VOG4955,lytic protein Rz1,Other +VOG4968,virion structural protein,Other +VOG4971,HTH DNA binding domain protein,Other +VOG4979,Vs valyl-tRNA synthetase modifier,Other +VOG4985,putative minor structural protein,Other +VOG4995,gp35,Other +VOG4999,DNA primase,Replication +VOG5008,glycerophosphoryl diesterphosphodiesterase,Other +VOG5012,portal protein,Portal +VOG5022,putative site-specific intron-like DNA endonuclease,Other +VOG5024,tail assembly protein,Assembly +VOG5027,head morphogeneis protein,Other +VOG5031,lysin,Lysis +VOG5032,virion-associated phage protein,Other +VOG5035,CHAP domain protein,Other +VOG5036,DarB-like antirestriction protein,Other +VOG5046,replication protein,Replication +VOG5052,partition protein ParB,Other +VOG5053,putative gp37,Other +VOG5055,gp10,Other +VOG5062,gp13,Other +VOG5063,putative transcriptional regulator,Other +VOG5083,DarB,Other +VOG5084,Ant1,Other +VOG5085,"gp41, hypothetical protein",Other +VOG5086,gp43,Other +VOG5088,putative transposase,Integration +VOG5089,putative phage repressor,Other +VOG5091,cytosine-specific DNA methyltransferase,Other +VOG5095,gp61,Other +VOG5096,gp23,Other +VOG5098,gp33,Other +VOG5100,tail fiber,Tail +VOG5101,gp10,Other +VOG5106,phage terminase large subunit,Terminase +VOG5116,putative endonuclease,Other +VOG5118,gp50,Other +VOG5121,DNA methylase,Other +VOG5125,gp20,Other +VOG5126,putative bifunctional DNA primase/polymerase,Replication +VOG5127,tail assembly chaperone,Assembly +VOG5148,metal-dependent hydrolase,Other +VOG5156,gp4,Other +VOG5162,Ro protein,Other +VOG5170,putative DNA-PolB associated exonuclease,Other +VOG5173,putative tail fiber,Tail +VOG5188,tapemeasure,Other +VOG5196,gp205,Other +VOG5203,HNH endonuclease domain protein,Other +VOG5211,structural protein,Other +VOG5213,membrane protein,Other +VOG5214,structural protein,Other +VOG5227,replicative clamp,Replication +VOG5231,6-phosphogluconate dehydrogenase,Other +VOG5235,DNA polymerase III beta subunit,Replication +VOG5239,restriction endonuclease,Other +VOG5249,TreO,Other +VOG5255,putative head stabilization/decoration protein,Other +VOG5260,tail fiber,Tail +VOG5268,tail fiber protein,Tail +VOG5280,replication terminator protein,Replication +VOG5302,flavodoxin,Other +VOG5305,putative DNA methylase,Other +VOG5329,TreB,Other +VOG5332,putative peptidase,Other +VOG5345,holin,Lysis +VOG5372,neck passage structure protein,Other +VOG5392,transposase-like protein,Integration +VOG5435,putative outer membrane protein,Other +VOG5441,colanic acid-degrading protein,Other +VOG5443,Kil protein,Other +VOG5447,positive control sigma-like factor,Other +VOG5448,putative peptidyl-tRNA hydrolase,Other +VOG5456,TreA,Other +VOG5477,holin,Lysis +VOG5478,head-tail adaptor,Other +VOG5481,NAD-dependent DNA ligase subunit B,Replication +VOG5511,tail fiber protein,Tail +VOG5520,pre-TMP frameshift protein,Other +VOG5551,RNAse H,Other +VOG5556,pre-tape measure frameshift protein G-T,Other +VOG5566,putative phage tail protein,Tail +VOG5573,putative terminase small subunit,Terminase +VOG5575,putative structural protein,Other +VOG5577,putative holin,Lysis +VOG5581,constituent protein,Other +VOG5584,major capsid & capsid maturation protease,Assembly +VOG5585,head-to-tail connector,Other (structural) +VOG5587,major tail protein,Tail +VOG5589,minor tail protein,Tail +VOG5590,major coat protein,Coat +VOG5593,gp23,Other +VOG5595,putative DNA primase/polymerase,Replication +VOG5604,portal protein,Portal +VOG5617,recombination protein U,Other +VOG5656,topoisomerase II large subunit,Replication +VOG5657,beta glucosyl transferase,Other +VOG5661,structural protein,Other +VOG5680,VI protein,Other +VOG5687,HTH DNA binding domain protein,Other +VOG5698,putative DNA N6-adenine methyltransferase,Other +VOG5700,gp18,Other +VOG5707,rare lipoprotein A,Other +VOG5742,putative regulatory protein,Other +VOG5751,putative phage DNA primase,Replication +VOG5769,structural protein,Other +VOG5775,AAA ATPase,Other +VOG5781,pectate lyase,Other +VOG5782,exonuclease,Other +VOG5786,structural protein,Other +VOG5793,tapemeasure,Other +VOG5794,gp26,Other +VOG5817,gp37,Other +VOG5818,gp65,Other +VOG5840,putative cell division control protein,Other +VOG5846,receptor-binding tail protein,Tail +VOG5861,putative short tail fiber,Tail +VOG5862,putative short tail fiber,Tail +VOG5871,putative minor structural protein 1,Other +VOG5902,putative lower collar protein,Other +VOG5904,putative cell wall hydrolase protein,Other +VOG5918,carboxypeptidase A,Other +VOG5938,putative primase,Replication +VOG5942,putative DNA replication protein,Replication +VOG5946,tail protein,Tail +VOG5950,recombinase,Other +VOG5953,internal head protein,Other +VOG5979,phospho-2-dehydro-3-deoxyheptonate aldolase,Other +VOG5982,homing endonuclease,Other +VOG5986,MazG,Other +VOG6001,prohead protease,Other +VOG6034,Appr-1-p processing protein,Other +VOG6042,putative tail fiber protein,Tail +VOG6058,putative encapsidation protein,Assembly +VOG6076,DNA pilot protein VP2,Other +VOG6085,putative DHH phosphoesterase protein,Other +VOG6131,HTH binding protein,Other +VOG6133,tail protein,Tail +VOG6152,putative pre-tape measure chaperone protein,Other +VOG6163,putative tape measure protein,Other +VOG6166,tail lysozyme,Tail +VOG6167,complement inhibitor,Other +VOG6170,DNA methylase,Other +VOG6193,putative endolysin,Lysis +VOG6196,coat protein,Coat +VOG6200,VP4 precursor,Other +VOG6207,DnaA protein,Other +VOG6230,receptor-blocking protein,Other +VOG6232,major capsid protein,Coat +VOG6236,methyltransferase,Other +VOG6246,putative structural protein,Other +VOG6247,antioxidant protein,Other +VOG6275,putative sporulation protein YhbH,Other +VOG6282,putative IS transposase (OrfA),Integration +VOG6288,putative DNA injection protein,Other +VOG6302,capsid maturation protease,Assembly +VOG6313,putative terminase small subunit,Terminase +VOG6314,receptor-binding protein,Other +VOG6331,cell wall peptidase,Other +VOG6343,portal protein,Portal +VOG6345,major capsid subunit,Coat +VOG6350,terminase large subunit,Terminase +VOG6371,LysM,Other +VOG6373,minor tail protein,Tail +VOG6389,conserved phage protein,Other +VOG6391,scaffolding protein,Other +VOG6396,DNA polymerase IV,Replication +VOG6422,abortive infection bacteriophage resistance protein,Other +VOG6427,pyruvate kinase,Other +VOG6449,peptide deformylase,Other +VOG6452,gpB,Other +VOG6457,virion structural protein,Other +VOG6465,Rz,Other +VOG6479,transcriptional regulator,Other +VOG6488,terminase large subunit,Terminase +VOG6513,chaperonin GroEL,Other +VOG6520,RecE,Other +VOG6535,baseplate wedge subunit,Baseplate +VOG6537,gp11,Other +VOG6540,putative adsorption protein,Other +VOG6551,lysozyme,Other +VOG6560,von Willebrand factor domain protein,Other +VOG6565,putative holin,Lysis +VOG6566,EaC protein,Other +VOG6568,putative tail fiber protein,Tail +VOG6599,putative DNAse/helicase protein,Replication +VOG6602,LAGLIDADG endonuclease,Other +VOG6628,AbrB family transcriptional regulator,Other +VOG6632,putative transcriptional activator,Other +VOG6633,putative tail protein,Tail +VOG6648,HTH DNA binding protein,Other +VOG6667,DNA primase,Replication +VOG6669,cell wall hydrolase,Other +VOG6672,minor structural protein,Other +VOG6676,DNA primase,Replication +VOG6751,tail connector protein,Other (structural) +VOG6796,PE/PPE-like protein,Other +VOG6813,acetyltransferase,Other +VOG6815,bacteriocin biosynthesis protein,Other +VOG6821,putative rIIa-like protein,Other +VOG6822,putative DNA polymerase,Replication +VOG6823,Cro-like protein,Other +VOG6857,gp42,Other +VOG6879,lytic protein Rz,Other +VOG6888,DNA polymerase III subunit beta,Replication +VOG6912,LysA,Other +VOG6924,putative 2-component regulator,Other +VOG6942,QueF,Other +VOG6945,putative transcriptional regulator,Other +VOG6965,"transposase InsH, IS5D, IS5 family",Integration +VOG6967,CRO protein,Other +VOG6975,YolD-like protein,Other +VOG6988,putative glucose-1-phosphate thymidylyltransferase,Other +VOG7037,putative base plate lysozyme,Other +VOG7054,adhesin,Other +VOG7066,structural protein,Other +VOG7067,chaperonin cpn10,Other +VOG7069,structural protein,Other +VOG7071,structural protein,Other +VOG7073,structural protein,Other +VOG7074,structural protein,Other +VOG7075,structural protein,Other +VOG7089,tailspike,Tail +VOG7099,DNA polymerase,Replication +VOG7104,phage tail fiber protein,Tail +VOG7110,HicA-like protein,Other +VOG7125,putative transcriptional regulator,Other +VOG7137,gene transfer agent,Other +VOG7152,minor tail protein,Tail +VOG7154,MutT/NUDIX hydrolase family protein,Other +VOG7167,putative holin,Lysis +VOG7168,bacterial surface protein,Other +VOG7172,RNA polymerase ECF sigma factor,Other +VOG7188,phosphoribosyl transferase,Other +VOG7232,tail assembly chaperone,Assembly +VOG7238,phage tail protein,Tail +VOG7243,tail fiber protein,Tail +VOG7260,Tail fiber protein,Tail +VOG7264,DNA primase,Replication +VOG7266,putative IS transposase (OrfB),Integration +VOG7274,putative transglutaminase-like cysteine peptidase,Other +VOG7277,putative minor capsid protein,Coat +VOG7279,putative lectin-like domain protein,Other +VOG7284,putative tail protein,Tail +VOG7285,putative tail protein,Tail +VOG7286,putative holin protein,Lysis +VOG7287,putative inner membrane spanin component,Other +VOG7288,putative outer membrane spanin component,Other +VOG7298,putative HTH domain protein,Other +VOG7302,putative TAT signal protein,Other +VOG7312,terminase small subunit,Terminase +VOG7318,putative ArdC-like antirestriction protein,Other +VOG7320,structural protein,Other +VOG7321,structural protein,Other +VOG7325,portal protein,Portal +VOG7329,tape measure,Other +VOG7340,potassium voltage-gated channel subfamily A member 1 protein,Other +VOG7364,putative small terminase subunit,Terminase +VOG7391,tail assembly chaperone,Assembly +VOG7403,putative portal protein,Portal +VOG7405,putative rIIb-like protein,Other +VOG7407,intein-containing putative terminase large subunit precursor,Terminase +VOG7415,baseplate hub subunit,Baseplate +VOG7416,putative HNH endonuclease inducing intron mobility,Other +VOG7417,phage head-tail joining protein,Other (structural) +VOG7419,RNA polymerase-ADP-ribosyltransferase Alt,Other +VOG7421,DNA binding protein,Other +VOG7424,putative phage-related hydrogenase,Other +VOG7428,scaffolding protein,Other +VOG7430,virion structural protein,Other +VOG7434,staphylokinase,Other +VOG7435,chemotaxis-inhibiting protein CHIPS,Other +VOG7437,TerB,Other +VOG7440,long tail fiber distal subunit adhesine,Tail +VOG7442,putative ABC transporter ATP-binding protein,Other +VOG7443,ea59,Other +VOG7444,putative DNA polymerase,Replication +VOG7451,AlpA-like transcriptional regulator,Other +VOG7454,methyltransferase,Other +VOG7456,ATP-dependent metalloprotease,Other +VOG7495,putative tail protein,Tail +VOG7497,major capsid protein,Coat +VOG7503,putative amidotransferase,Other +VOG7511,terminase small subunit,Terminase +VOG7515,tRNA (cmo5U34)-methyltransferase,Other +VOG7516,EaI protein,Other +VOG7554,RecA-like recombination protein,Other +VOG7563,glycosyltransferase-family protein,Other +VOG7569,gp19,Other +VOG7575,virion structural protein,Other +VOG7581,cI-like putative transcriptional regulator,Other +VOG7606,phycobilisome degredation protein,Other +VOG7623,VP4,Other +VOG7629,putative phage structural protein,Other +VOG7633,putative HD domain protein,Other +VOG7641,type II restriction enzyme BsuBI,Other +VOG7642,modification methylase BsuBI,Other +VOG7652,putative virion structural protein,Other +VOG7687,gp51,Other +VOG7689,gp31,Other +VOG7695,structural protein,Other +VOG7701,RstB,Other +VOG7718,YomR-like protein,Other +VOG7767,RIIA-like protein,Other +VOG7789,putative tail fiber,Tail +VOG7808,conserved hypothetical protein (XkdN-like),Other +VOG7823,tail sheath,Tail +VOG7880,aerobic NDP reductase small subunit,Other +VOG7884,putative DNA segregation ATPase FtsK/SpoIIIE,Other +VOG7887,PemK-like protein,Other +VOG7900,tail spike protein,Tail +VOG7907,gp10,Other +VOG7913,gp25,Other +VOG7917,RNA polymerase sigma factor,Other +VOG7941,replication factor C small subunit,Replication +VOG7946,Mu F-like capsid morphogenesis protein,Other +VOG7961,virion structural protein,Other +VOG7962,putative holin,Lysis +VOG7981,regulator of chromosome condensation RCC1,Other +VOG8001,putative lysozyme,Other +VOG8004,tail sheath protein,Tail +VOG8023,putative virion protein and lysozyme murein,Other +VOG8085,methyltransferase,Other +VOG8134,putative tail fiber protein 1,Tail +VOG8138,major capsid protein,Coat +VOG8163,VRR-NUC domain containing protein,Other +VOG8165,DNA methylase,Other +VOG8166,putative glycosyltransferase,Other +VOG8169,head-tail connector protein,Other (structural) +VOG8171,putative tail length tape measure protein,Tail +VOG8172,structural protein,Other +VOG8173,structural protein,Other +VOG8187,head outer capsid protein,Coat +VOG8215,gp165,Other +VOG8216,base plate lysozyme,Other +VOG8218,integrase,Integration +VOG8223,putative tail fiber protein,Tail +VOG8226,terminase small subunit,Terminase +VOG8237,HNH endonuclease,Other +VOG8238,putative DNA endonuclease VII,Other +VOG8244,"site specific recombinase, tyrosine",Other +VOG8257,RNA polymerase sigma factor,Other +VOG8262,phage tail protein,Tail +VOG8290,major coat protein,Coat +VOG8295,LydD,Other +VOG8296,OdaA,Other +VOG8297,PmgA,Other +VOG8298,RepA,Other +VOG8299,ShtB,Other +VOG8303,putative S-adenosylmethionine synthetase,Other +VOG8306,putative envelope protein,Other +VOG8313,gp8,Other +VOG8314,gp11,Other +VOG8315,gp15,Other +VOG8316,gp21,Other +VOG8317,gp23,Other +VOG8332,virion protein,Other +VOG8343,putative tail fiber,Tail +VOG8384,peptidase-like protein,Other +VOG8387,transposase,Integration +VOG8389,capsid and scaffold protein,Other +VOG8414,PblB-type protein,Other +VOG8438,minor capsid protein,Coat +VOG8473,RNA polymerase sigma factor,Other +VOG8487,transcription regulatory protein,Other +VOG8492,zinc-ribbon domain-containing protein,Other +VOG8495,internal virion protein,Other +VOG8498,PCNA protein,Other +VOG8502,virion structural protein,Other +VOG8506,RNA polymerase sigma-70 factor,Other +VOG8516,virion-associated phage protein,Other +VOG8519,holin,Lysis +VOG8520,helix-turn-helix domain protein,Other +VOG8534,high light inducible protein,Other +VOG8536,phosphohydrolase,Other +VOG8549,tail protein,Tail +VOG8550,PfWMP3_27,Other +VOG8551,tail tubular protein B,Tail +VOG8552,tail tubular protein A,Tail +VOG8553,scaffold protein,Other +VOG8556,enterotoxin type A precursor,Other +VOG8557,160 kDa protein,Other +VOG8578,putative virion structural protein,Other +VOG8579,tailspike protein,Tail +VOG8586,gp63,Other +VOG8599,thymidylate synthase,Other +VOG8607,ribonucleotide diphosphate reductas alpha subunit,Other +VOG8609,structural protein,Other +VOG8616,NAD+ synthetase,Other +VOG8617,putative tail fiber adhesion protein,Tail +VOG8625,terminase small subunit,Terminase +VOG8643,putative ribosomal-protein-alanine N-acetyltransferase,Other +VOG8650,pre-neck appendage protein,Other +VOG8651,putative lysozyme-peptidase,Other +VOG8653,putative DNA modification methylase,Other +VOG8678,putative aminoacyl-tRNA hydrolase,Other +VOG8684,tail fiber protein,Tail +VOG8687,possible virion structural protein,Other +VOG8725,carboxylesterase,Other +VOG8726,phenylalanyl-tRNA synthetase subunit beta,Other +VOG8742,chaperonin cpn10,Other +VOG8751,structural protein,Other +VOG8752,structural protein,Other +VOG8754,structural protein,Other +VOG8779,NifU-like protein,Other +VOG8783,gp63,Other +VOG8820,beta-glucanase,Other +VOG8849,gp42,Other +VOG8850,gp101,Other +VOG8855,DNA polymerase,Replication +VOG8863,helix-turn-helix XRE-family of transcriptional regulators,Other +VOG8866,thymidylate kinase,Other +VOG8868,major tail protein extension,Tail +VOG8870,pIII-CTX,Other +VOG8877,putative regulatory protein,Other +VOG8882,major tail protein,Tail +VOG8888,RecA-like recombinase,Other +VOG8899,virion structural protein,Other +VOG8905,nonstructural protein,Other +VOG8909,HNH protein,Other +VOG8916,putative transposase,Integration +VOG8925,Gp40 protein,Other +VOG8926,Gp41 protein,Other +VOG8954,Gp7 protein,Other +VOG8985,putative dehalogenase hydrolase-like protein,Other +VOG8986,putative phosphoribosyltransferase-like domain protein,Other +VOG8992,"putative dTDP-4-dehydrorhamnose 3,5-epimerase",Other +VOG9038,tail assembly chaperone,Assembly +VOG9064,putative virion structural protein 19,Other +VOG9086,internal virion protein,Other +VOG9093,putative RNA 2'-phosphotransferase,Other +VOG9099,putative NAD+ diphosphatase,Other +VOG9115,primase/polymerase,Replication +VOG9191,Cre,Other +VOG9192,portal vertex protein of head,Portal +VOG9193,LydA,Other +VOG9195,Phd,Other +VOG9203,membrane protein,Other +VOG9209,minor tail protein L,Tail +VOG9211,LysB,Other +VOG9234,putative DNA binding protein,Other +VOG9237,tail fiber protein,Tail +VOG9243,putative nicotinamide mononucleotide transporter,Other +VOG9244,putative tail protein,Tail +VOG9258,tape measure,Other +VOG9259,tail fiber protein,Tail +VOG9260,structural protein,Other +VOG9261,deaminase,Other +VOG9262,prohead protease,Other +VOG9274,middle expressed protein 4,Other +VOG9286,putative bacterial RNA polymerase inhibitor,Other +VOG9288,glycosidase,Other +VOG9305,EaD protein,Other +VOG9306,tail fiber protein,Tail +VOG9308,phage DNA end protector during packaging,Other +VOG9310,HNH endonuclease domain protein,Other +VOG9315,terminase large subunit,Terminase +VOG9322,HNH endonuclease,Other +VOG9323,putative major tail protein,Tail +VOG9325,immunoglobulin I-set domain protein,Other +VOG9328,tail protein,Tail +VOG9339,minor tail protein Z,Tail +VOG9340,tail fiber protein,Tail +VOG9348,tail fiber protein,Tail +VOG9358,C8,Other +VOG9359,Mat,Other +VOG9360,putative protein Ulx,Other +VOG9361,Pro,Other +VOG9362,"conserved protein of unknown function, DdrB",Other +VOG9363,Upf26.7,Other +VOG9364,DarA,Other +VOG9365,conserved protein of unknown function Hdf,Other +VOG9366,LydB,Other +VOG9367,gpR,Other +VOG9368,gp16,Other +VOG9369,PmgB,Other +VOG9370,major tail tube protein TubB,Tail +VOG9371,PmgC,Other +VOG9373,putative outer membrane lipoprotein,Other +VOG9374,Icd,Other +VOG9375,RepL,Other +VOG9376,Upf52.7,Other +VOG9377,upf54.2,Other +VOG9378,tail sheath protein Gp22,Tail +VOG9379,Upf57.5,Other +VOG9380,Upf62.7,Other +VOG9381,conserved protein of unknown function UpfB,Other +VOG9382,Upf64.0,Other +VOG9383,Dbn,Other +VOG9384,gp6,Other +VOG9385,Upf78.5,Other +VOG9386,gp7,Other +VOG9387,gp25,Other +VOG9388,gp26,Other +VOG9389,PmgN,Other +VOG9390,putative morphogenetic protein PmgP,Other +VOG9391,HdmD,Other +VOG9392,PmgR,Other +VOG9393,Fdc,Other +VOG9394,Lpa,Other +VOG9395,PacA,Other +VOG9396,C1.100,Other +VOG9397,Coi,Other +VOG9404,YolD-like protein,Other +VOG9410,ea8.5,Other +VOG9414,putative mitochondrial DNA polymerase gamma homologue,Replication +VOG9415,putative DNA primase,Replication +VOG9417,DNA polymerase I-like flap endonuclease (FEN),Replication +VOG9420,IS1 transposase B,Integration +VOG9425,putative minor coat protein,Coat +VOG9429,gp74,Other +VOG9431,gp87,Other +VOG9433,gp114,Other +VOG9434,gp135,Other +VOG9437,gp59,Other +VOG9438,HNH endonuclease,Other +VOG9446,gp20,Other +VOG9447,gp51,Other +VOG9453,gp97,Other +VOG9454,lytic conversion lipoprotein precursor,Other +VOG9462,BofR,Other +VOG9475,head-tail connector,Other (structural) +VOG9481,nucleoid-associated protein,Other +VOG9485,structural protein,Other +VOG9487,structural protein,Other +VOG9493,holin,Lysis +VOG9502,putative lysin,Lysis +VOG9509,membrane protein,Other +VOG9532,glycosyl transferase group I,Other +VOG9534,structural protein,Other +VOG9539,putative amidotransferase,Other +VOG9551,plasmid maintenance system killer HigB,Other +VOG9556,holin,Lysis +VOG9563,capsid and scaffold protein,Other +VOG9572,core encoded pilin,Other +VOG9573,accessory cholera enterotoxin,Other +VOG9586,terminase large subunit,Terminase +VOG9588,tail protein P,Tail +VOG9629,formamidopyrimidine-DNA glycosylase,Other +VOG9632,putative head-tail connector protein,Other (structural) +VOG9639,Conserved hypothetical,Other +VOG9657,lysophospholipase L1-related esterase,Other +VOG9659,endolysin,Lysis +VOG9661,acetyltransferase domain protein,Other +VOG9663,HNH endonuclease domain protein,Other +VOG9667,XRE family transcriptional regulator,Other +VOG9686,S-layer domain-containing protein,Other +VOG9690,Hypothetical-Protein ,Other +VOG9697,sulfotransferase,Other +VOG9701,gp5,Other +VOG9702,gp69,Other +VOG9705,palmitoyltransferase,Other +VOG9709,Ea47 protein,Other +VOG9710,Ea31 protein,Other +VOG9712,putative excinuclease ABC,Other +VOG9717,minor coat protein,Coat +VOG9718,gp37,Other +VOG9719,gp38,Other +VOG9720,gp39,Other +VOG9721,gp41,Other +VOG9722,gp45,Other +VOG9723,gp47,Other +VOG9724,gp51,Other +VOG9725,Phage repressor,Other +VOG9726,gp2,Other +VOG9727,gp4,Other +VOG9728,gp15,Other +VOG9729,gp18,Other +VOG9730,gp22,Other +VOG9731,gp23,Other +VOG9732,gp25,Other +VOG9733,nonstructural protein,Other +VOG9736,O-antigen beta polymerase,Replication +VOG9738,putative transcriptional regulator,Other +VOG9740,ssDNA-binding,Other +VOG9741,putative repressor,Other +VOG9746,gp23,Other +VOG9747,gp28,Other +VOG9761,gp34.26,Other +VOG9771,gp34 protein,Other +VOG9773,gp03 protein,Other +VOG9778,virion structural protein,Other +VOG9787,putative Kelch-like ECH-associated protein,Other +VOG9788,virion structural protein,Other +VOG9789,virion structural protein,Other +VOG9790,virion structural protein,Other +VOG9791,virion structural protein,Other +VOG9792,virion structural protein,Other +VOG9793,virion structural protein,Other +VOG9795,virion structural protein,Other +VOG9797,virion structural protein,Other +VOG9798,virion structural protein,Other +VOG9799,virion structural protein,Other +VOG9803,virion structural protein,Other +VOG9804,virion structural protein,Other +VOG9809,virion structural protein,Other +VOG9810,virion structural protein,Other +VOG9821,putative nucleotidyltransferase protein,Other +VOG9834,gp59,Other +VOG9836,gp29,Other +VOG9839,putative Fe-S oxidoreductase,Other +VOG9857,gp11,Other +VOG9869,Hypothetical-Protein ,Other +VOG9873,tail fiber-like protein,Tail +VOG9876,PRGA-formyltransferase,Other +VOG9904,putative protein 2,Other +VOG9915,VP13,Other +VOG9916,VP2,Other +VOG9917,capsid protein VP5,Coat +VOG9922,putative protein 31,Other +VOG9924,putative protein 33,Other +VOG9941,putative terminase large subunit-like protein,Terminase +VOG9948,gp38,Other +VOG9957,C-terminal part of the MCM2-like helicase,Replication +VOG9959,capsid and scaffold protein,Other +VOG9995,tail fiber protein,Tail +VOG10005,putative antirestriction protein,Other +VOG10009,putative tail fiber,Tail +VOG10016,tail assembly protein,Assembly +VOG10022,baseplate wedge initiator,Baseplate +VOG10023,putative topoisomerasae I protein,Replication +VOG10026,putative ATPase,Other +VOG10038,trypsin-like serine protease domain protein,Other +VOG10044,gp14-like protein,Other +VOG10059,antirepressor,Other +VOG10065,gp18.5,Other +VOG10069,capsid protein,Coat +VOG10080,glycerophosphodiester phosphodiesterase,Other +VOG10086,baseplate wedge subunit,Baseplate +VOG10088,DNA primase,Replication +VOG10095,putative quaternary ammonium compound-resistance protein qacE,Other +VOG10106,gp134,Other +VOG10155,Very-short-patch mismatch repair endonuclease,Other +VOG10157,putative cytoplasmic protein,Other +VOG10158,alkaline phosphatase,Other +VOG10195,putative DNA binding excisionase protein,Other +VOG10217,metallo-beta-lactamase domain-containing protein,Other +VOG10224,putative SpoVG protein,Other +VOG10227,terminase large subunit,Terminase +VOG10254,CobS porphyrin biosynthetic protein,Other +VOG10264,putative tail fiber protein,Tail +VOG10277,Possible tail sheath protein,Tail +VOG10284,Possible phage tail tube protein,Tail +VOG10285,putative transketolase,Other +VOG10286,putative N-acetylneuraminate pyruvate lyase,Other +VOG10292,putative minor tail assembly protein,Assembly +VOG10294,putative UDP-glucose dehydrogenase,Other +VOG10330,putative holin,Lysis +VOG10342,HicB protein,Other +VOG10343,tail fiber protein,Tail +VOG10352,putative acetyltransferase,Other +VOG10371,putative radical SAM superfamily protein 2,Other +VOG10429,Hef nuclease,Other +VOG10443,replication factor C large subunit,Replication +VOG10448,RadA,Other +VOG10452,portal protein,Portal +VOG10453,gpF-like protein,Other +VOG10454,zeta toxin domain protein,Other +VOG10456,major capsid protein,Coat +VOG10460,tail assembly chaperone,Assembly +VOG10462,RNAse HI,Other +VOG10471,DNA polymerase,Replication +VOG10512,major capsid protein,Coat +VOG10520,tail fiber protein,Tail +VOG10522,DUF3800 domain-containing protein,Other +VOG10538,structural protein,Other +VOG10544,VirE N-domain protein,Other +VOG10570,gp77,Other +VOG10596,putative primase,Replication +VOG10608,prophage protein,Other +VOG10633,gp004,Other +VOG10634,gp80,Other +VOG10636,gp241,Other +VOG10637,gp1,Other +VOG10638,gp44,Other +VOG10641,gp35,Other +VOG10654,tail tape measure chaperone protein,Tail +VOG10666,BTLCP-like protein,Other +VOG10674,terminase large subunit,Terminase +VOG10717,putative protein containing Nos-D like domain,Other +VOG10719,peptidase M15,Other +VOG10724,putative homing endonuclease,Other +VOG10737,elongation factor Ts-like protein,Other +VOG10738,S-adenosylmethionine decarboxylase-like protein,Other +VOG10739,putative peptidase-like protein,Other +VOG10763,signal peptide protein,Other +VOG10787,RelA/SpoT family protein,Other +VOG10842,terminase small subunit,Terminase +VOG10856,DNA topoisomerase II large subunit C-terminal region,Replication +VOG10861,gp22,Other +VOG10868,minor capsid protein,Coat +VOG10870,putative Transcription initiation factor B,Other +VOG10880,packaging NTPase P4,Other +VOG10883,gpJ,Other +VOG10887,RNA ligase 2,Other +VOG10898,gp15,Other +VOG10909,putative tail fiber protein,Tail +VOG10914,chaperone protein DnaK,Other +VOG10915,capsid decoration protein,Coat +VOG10916,gp14,Other +VOG10917,prophage antirepressor,Other +VOG10920,gp35,Other +VOG10930,long tail fiber distal subunit,Tail +VOG10934,putative amidotransferase,Other +VOG10942,minor coat protein,Coat +VOG10943,gp19,Other +VOG10944,minor structural protein,Other +VOG10945,holin,Lysis +VOG10951,o-spanin,Other +VOG10953,gp38,Other +VOG10957,putative tail protein,Tail +VOG10962,tail protein,Tail +VOG10967,putative tail sheath protein,Tail +VOG10969,putative tail fiber protein,Tail +VOG10971,cytolethal distending toxin V B subunit,Other +VOG10972,minor structural protein gp58,Other +VOG10978,putative peptidase/serine protease,Other +VOG10979,DNA polymerase subunit III,Replication +VOG10986,adenosylribosyltransferase,Other +VOG10993,peptidase domain-containing protein,Other +VOG10995,head morphogenesis protein,Other +VOG11009,putative TROVE-like domain protein,Other +VOG11016,putative transcriptional regulator,Other +VOG11017,putative radical SAM superfamily protein 1,Other +VOG11026,scaffolding protein,Other +VOG11048,structural protein,Other +VOG11053,tape measure protein,Other +VOG11065,gp53 protein,Other +VOG11070,tail fiber protein,Tail +VOG11071,putative tape measure protein,Other +VOG11075,DNA-binding protein,Other +VOG11080,putative crossover junction endodeoxyribonuclease RusA,Other +VOG11081,Rec A-like recombinase,Other diff --git a/phigaro/to_html/pvogs_annotations.pickle b/phigaro/to_html/pvogs_annotations.pickle deleted file mode 100644 index 7ee8d04..0000000 --- a/phigaro/to_html/pvogs_annotations.pickle +++ /dev/null @@ -1,7030 +0,0 @@ -ccopy_reg -_reconstructor -p0 -(cpandas.core.frame -DataFrame -p1 -c__builtin__ -object -p2 -Ntp3 -Rp4 -(dp5 -S'_metadata' -p6 -(lp7 -sS'_typ' -p8 -S'dataframe' -p9 -sS'_data' -p10 -g0 -(cpandas.core.internals -BlockManager -p11 -g2 -Ntp12 -Rp13 -((lp14 -cpandas.core.indexes.base -_new_Index -p15 -(cpandas.core.indexes.base -Index -p16 -(dp17 -S'data' -p18 -cnumpy.core.multiarray -_reconstruct -p19 -(cnumpy -ndarray -p20 -(I0 -tp21 -S'b' -p22 -tp23 -Rp24 -(I1 -(I2 -tp25 -cnumpy -dtype -p26 -(S'O8' -p27 -I0 -I1 -tp28 -Rp29 -(I3 -S'|' -p30 -NNNI-1 -I-1 -I63 -tp31 -bI00 -(lp32 -S'function' -p33 -aS'group' -p34 -atp35 -bsS'name' -p36 -Nstp37 -Rp38 -ag15 -(g16 -(dp39 -g18 -g19 -(g20 -(I0 -tp40 -g22 -tp41 -Rp42 -(I1 -(I1474 -tp43 -g29 -I00 -(lp44 -S'VOG0001' -p45 -aS'VOG0002' -p46 -aS'VOG0005' -p47 -aS'VOG0006' -p48 -aS'VOG0007' -p49 -aS'VOG0009' -p50 -aS'VOG0013' -p51 -aS'VOG0015' -p52 -aS'VOG0016' -p53 -aS'VOG0018' -p54 -aS'VOG0019' -p55 -aS'VOG0025' -p56 -aS'VOG0026' -p57 -aS'VOG0028' -p58 -aS'VOG0030' -p59 -aS'VOG0031' -p60 -aS'VOG0034' -p61 -aS'VOG0035' -p62 -aS'VOG0037' -p63 -aS'VOG0038' -p64 -aS'VOG0040' -p65 -aS'VOG0046' -p66 -aS'VOG0049' -p67 -aS'VOG0050' -p68 -aS'VOG0051' -p69 -aS'VOG0052' -p70 -aS'VOG0054' -p71 -aS'VOG0058' -p72 -aS'VOG0061' -p73 -aS'VOG0067' -p74 -aS'VOG0083' -p75 -aS'VOG0085' -p76 -aS'VOG0088' -p77 -aS'VOG0092' -p78 -aS'VOG0106' -p79 -aS'VOG0136' -p80 -aS'VOG0156' -p81 -aS'VOG0166' -p82 -aS'VOG0167' -p83 -aS'VOG0168' -p84 -aS'VOG0169' -p85 -aS'VOG0170' -p86 -aS'VOG0171' -p87 -aS'VOG0172' -p88 -aS'VOG0173' -p89 -aS'VOG0174' -p90 -aS'VOG0175' -p91 -aS'VOG0176' -p92 -aS'VOG0177' -p93 -aS'VOG0178' -p94 -aS'VOG0183' -p95 -aS'VOG0189' -p96 -aS'VOG0202' -p97 -aS'VOG0205' -p98 -aS'VOG0209' -p99 -aS'VOG0221' -p100 -aS'VOG0227' -p101 -aS'VOG0234' -p102 -aS'VOG0236' -p103 -aS'VOG0237' -p104 -aS'VOG0249' -p105 -aS'VOG0253' -p106 -aS'VOG0254' -p107 -aS'VOG0258' -p108 -aS'VOG0259' -p109 -aS'VOG0261' -p110 -aS'VOG0263' -p111 -aS'VOG0265' -p112 -aS'VOG0273' -p113 -aS'VOG0274' -p114 -aS'VOG0275' -p115 -aS'VOG0281' -p116 -aS'VOG0284' -p117 -aS'VOG0285' -p118 -aS'VOG0286' -p119 -aS'VOG0287' -p120 -aS'VOG0288' -p121 -aS'VOG0292' -p122 -aS'VOG0293' -p123 -aS'VOG0295' -p124 -aS'VOG0296' -p125 -aS'VOG0298' -p126 -aS'VOG0299' -p127 -aS'VOG0300' -p128 -aS'VOG0312' -p129 -aS'VOG0320' -p130 -aS'VOG0334' -p131 -aS'VOG0337' -p132 -aS'VOG0350' -p133 -aS'VOG0351' -p134 -aS'VOG0355' -p135 -aS'VOG0356' -p136 -aS'VOG0372' -p137 -aS'VOG0377' -p138 -aS'VOG0382' -p139 -aS'VOG0384' -p140 -aS'VOG0393' -p141 -aS'VOG0397' -p142 -aS'VOG0400' -p143 -aS'VOG0402' -p144 -aS'VOG0408' -p145 -aS'VOG0409' -p146 -aS'VOG0410' -p147 -aS'VOG0412' -p148 -aS'VOG0419' -p149 -aS'VOG0420' -p150 -aS'VOG0421' -p151 -aS'VOG0436' -p152 -aS'VOG0443' -p153 -aS'VOG0451' -p154 -aS'VOG0452' -p155 -aS'VOG0454' -p156 -aS'VOG0456' -p157 -aS'VOG0457' -p158 -aS'VOG0459' -p159 -aS'VOG0460' -p160 -aS'VOG0461' -p161 -aS'VOG0462' -p162 -aS'VOG0463' -p163 -aS'VOG0464' -p164 -aS'VOG0465' -p165 -aS'VOG0466' -p166 -aS'VOG0471' -p167 -aS'VOG0473' -p168 -aS'VOG0474' -p169 -aS'VOG0475' -p170 -aS'VOG0476' -p171 -aS'VOG0477' -p172 -aS'VOG0480' -p173 -aS'VOG0485' -p174 -aS'VOG0493' -p175 -aS'VOG0496' -p176 -aS'VOG0499' -p177 -aS'VOG0505' -p178 -aS'VOG0509' -p179 -aS'VOG0510' -p180 -aS'VOG0529' -p181 -aS'VOG0544' -p182 -aS'VOG0545' -p183 -aS'VOG0559' -p184 -aS'VOG0566' -p185 -aS'VOG0567' -p186 -aS'VOG0568' -p187 -aS'VOG0569' -p188 -aS'VOG0571' -p189 -aS'VOG0574' -p190 -aS'VOG0577' -p191 -aS'VOG0582' -p192 -aS'VOG0588' -p193 -aS'VOG0602' -p194 -aS'VOG0603' -p195 -aS'VOG0609' -p196 -aS'VOG0612' -p197 -aS'VOG0614' -p198 -aS'VOG0615' -p199 -aS'VOG0639' -p200 -aS'VOG0641' -p201 -aS'VOG0642' -p202 -aS'VOG0643' -p203 -aS'VOG0644' -p204 -aS'VOG0645' -p205 -aS'VOG0647' -p206 -aS'VOG0668' -p207 -aS'VOG0676' -p208 -aS'VOG0681' -p209 -aS'VOG0691' -p210 -aS'VOG0692' -p211 -aS'VOG0694' -p212 -aS'VOG0697' -p213 -aS'VOG0698' -p214 -aS'VOG0703' -p215 -aS'VOG0705' -p216 -aS'VOG0707' -p217 -aS'VOG0720' -p218 -aS'VOG0731' -p219 -aS'VOG0739' -p220 -aS'VOG0756' -p221 -aS'VOG0764' -p222 -aS'VOG0765' -p223 -aS'VOG0785' -p224 -aS'VOG0796' -p225 -aS'VOG0799' -p226 -aS'VOG0816' -p227 -aS'VOG0823' -p228 -aS'VOG0827' -p229 -aS'VOG0828' -p230 -aS'VOG0830' -p231 -aS'VOG0831' -p232 -aS'VOG0832' -p233 -aS'VOG0833' -p234 -aS'VOG0835' -p235 -aS'VOG0837' -p236 -aS'VOG0838' -p237 -aS'VOG0839' -p238 -aS'VOG0840' -p239 -aS'VOG0842' -p240 -aS'VOG0843' -p241 -aS'VOG0847' -p242 -aS'VOG0848' -p243 -aS'VOG0850' -p244 -aS'VOG0855' -p245 -aS'VOG0875' -p246 -aS'VOG0876' -p247 -aS'VOG0877' -p248 -aS'VOG0878' -p249 -aS'VOG0879' -p250 -aS'VOG0880' -p251 -aS'VOG0885' -p252 -aS'VOG0886' -p253 -aS'VOG0887' -p254 -aS'VOG0889' -p255 -aS'VOG0890' -p256 -aS'VOG0897' -p257 -aS'VOG0906' -p258 -aS'VOG0913' -p259 -aS'VOG0924' -p260 -aS'VOG0930' -p261 -aS'VOG0933' -p262 -aS'VOG0944' -p263 -aS'VOG0945' -p264 -aS'VOG0946' -p265 -aS'VOG0947' -p266 -aS'VOG0975' -p267 -aS'VOG0976' -p268 -aS'VOG0979' -p269 -aS'VOG0985' -p270 -aS'VOG0986' -p271 -aS'VOG0991' -p272 -aS'VOG0992' -p273 -aS'VOG0996' -p274 -aS'VOG0997' -p275 -aS'VOG0998' -p276 -aS'VOG1001' -p277 -aS'VOG1005' -p278 -aS'VOG1006' -p279 -aS'VOG1020' -p280 -aS'VOG1026' -p281 -aS'VOG1030' -p282 -aS'VOG1031' -p283 -aS'VOG1032' -p284 -aS'VOG1036' -p285 -aS'VOG1045' -p286 -aS'VOG1051' -p287 -aS'VOG1072' -p288 -aS'VOG1092' -p289 -aS'VOG1099' -p290 -aS'VOG1105' -p291 -aS'VOG1112' -p292 -aS'VOG1113' -p293 -aS'VOG1146' 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-aS'VOG9659' -p1328 -aS'VOG9661' -p1329 -aS'VOG9663' -p1330 -aS'VOG9667' -p1331 -aS'VOG9686' -p1332 -aS'VOG9690' -p1333 -aS'VOG9697' -p1334 -aS'VOG9701' -p1335 -aS'VOG9702' -p1336 -aS'VOG9705' -p1337 -aS'VOG9709' -p1338 -aS'VOG9710' -p1339 -aS'VOG9712' -p1340 -aS'VOG9717' -p1341 -aS'VOG9718' -p1342 -aS'VOG9719' -p1343 -aS'VOG9720' -p1344 -aS'VOG9721' -p1345 -aS'VOG9722' -p1346 -aS'VOG9723' -p1347 -aS'VOG9724' -p1348 -aS'VOG9725' -p1349 -aS'VOG9726' -p1350 -aS'VOG9727' -p1351 -aS'VOG9728' -p1352 -aS'VOG9729' -p1353 -aS'VOG9730' -p1354 -aS'VOG9731' -p1355 -aS'VOG9732' -p1356 -aS'VOG9733' -p1357 -aS'VOG9736' -p1358 -aS'VOG9738' -p1359 -aS'VOG9740' -p1360 -aS'VOG9741' -p1361 -aS'VOG9746' -p1362 -aS'VOG9747' -p1363 -aS'VOG9761' -p1364 -aS'VOG9771' -p1365 -aS'VOG9773' -p1366 -aS'VOG9778' -p1367 -aS'VOG9787' -p1368 -aS'VOG9788' -p1369 -aS'VOG9789' -p1370 -aS'VOG9790' -p1371 -aS'VOG9791' -p1372 -aS'VOG9792' -p1373 -aS'VOG9793' -p1374 -aS'VOG9795' -p1375 -aS'VOG9797' -p1376 -aS'VOG9798' -p1377 -aS'VOG9799' -p1378 -aS'VOG9803' -p1379 -aS'VOG9804' -p1380 -aS'VOG9809' -p1381 -aS'VOG9810' -p1382 -aS'VOG9821' -p1383 -aS'VOG9834' -p1384 -aS'VOG9836' -p1385 -aS'VOG9839' -p1386 -aS'VOG9857' -p1387 -aS'VOG9869' -p1388 -aS'VOG9873' -p1389 -aS'VOG9876' -p1390 -aS'VOG9904' -p1391 -aS'VOG9915' -p1392 -aS'VOG9916' -p1393 -aS'VOG9917' -p1394 -aS'VOG9922' -p1395 -aS'VOG9924' -p1396 -aS'VOG9941' -p1397 -aS'VOG9948' -p1398 -aS'VOG9957' -p1399 -aS'VOG9959' -p1400 -aS'VOG9995' -p1401 -aS'VOG10005' -p1402 -aS'VOG10009' -p1403 -aS'VOG10016' -p1404 -aS'VOG10022' -p1405 -aS'VOG10023' -p1406 -aS'VOG10026' -p1407 -aS'VOG10038' -p1408 -aS'VOG10044' -p1409 -aS'VOG10059' -p1410 -aS'VOG10065' -p1411 -aS'VOG10069' -p1412 -aS'VOG10080' -p1413 -aS'VOG10086' -p1414 -aS'VOG10088' -p1415 -aS'VOG10095' -p1416 -aS'VOG10106' -p1417 -aS'VOG10155' -p1418 -aS'VOG10157' -p1419 -aS'VOG10158' -p1420 -aS'VOG10195' -p1421 -aS'VOG10217' -p1422 -aS'VOG10224' -p1423 -aS'VOG10227' -p1424 -aS'VOG10254' -p1425 -aS'VOG10264' -p1426 -aS'VOG10277' -p1427 -aS'VOG10284' -p1428 -aS'VOG10285' -p1429 -aS'VOG10286' -p1430 -aS'VOG10292' -p1431 -aS'VOG10294' -p1432 -aS'VOG10330' -p1433 -aS'VOG10342' -p1434 -aS'VOG10343' -p1435 -aS'VOG10352' -p1436 -aS'VOG10371' -p1437 -aS'VOG10429' -p1438 -aS'VOG10443' -p1439 -aS'VOG10448' -p1440 -aS'VOG10452' -p1441 -aS'VOG10453' -p1442 -aS'VOG10454' -p1443 -aS'VOG10456' -p1444 -aS'VOG10460' -p1445 -aS'VOG10462' -p1446 -aS'VOG10471' -p1447 -aS'VOG10512' -p1448 -aS'VOG10520' -p1449 -aS'VOG10522' -p1450 -aS'VOG10538' -p1451 -aS'VOG10544' -p1452 -aS'VOG10570' -p1453 -aS'VOG10596' -p1454 -aS'VOG10608' -p1455 -aS'VOG10633' -p1456 -aS'VOG10634' -p1457 -aS'VOG10636' -p1458 -aS'VOG10637' -p1459 -aS'VOG10638' -p1460 -aS'VOG10641' -p1461 -aS'VOG10654' -p1462 -aS'VOG10666' -p1463 -aS'VOG10674' -p1464 -aS'VOG10717' -p1465 -aS'VOG10719' -p1466 -aS'VOG10724' -p1467 -aS'VOG10737' -p1468 -aS'VOG10738' -p1469 -aS'VOG10739' -p1470 -aS'VOG10763' -p1471 -aS'VOG10787' -p1472 -aS'VOG10842' -p1473 -aS'VOG10856' -p1474 -aS'VOG10861' -p1475 -aS'VOG10868' -p1476 -aS'VOG10870' -p1477 -aS'VOG10880' -p1478 -aS'VOG10883' -p1479 -aS'VOG10887' -p1480 -aS'VOG10898' -p1481 -aS'VOG10909' -p1482 -aS'VOG10914' -p1483 -aS'VOG10915' -p1484 -aS'VOG10916' -p1485 -aS'VOG10917' -p1486 -aS'VOG10920' -p1487 -aS'VOG10930' -p1488 -aS'VOG10934' -p1489 -aS'VOG10942' -p1490 -aS'VOG10943' -p1491 -aS'VOG10944' -p1492 -aS'VOG10945' -p1493 -aS'VOG10951' -p1494 -aS'VOG10953' -p1495 -aS'VOG10957' -p1496 -aS'VOG10962' -p1497 -aS'VOG10967' -p1498 -aS'VOG10969' -p1499 -aS'VOG10971' -p1500 -aS'VOG10972' -p1501 -aS'VOG10978' -p1502 -aS'VOG10979' -p1503 -aS'VOG10986' -p1504 -aS'VOG10993' -p1505 -aS'VOG10995' -p1506 -aS'VOG11009' -p1507 -aS'VOG11016' -p1508 -aS'VOG11017' -p1509 -aS'VOG11026' -p1510 -aS'VOG11048' -p1511 -aS'VOG11053' -p1512 -aS'VOG11065' -p1513 -aS'VOG11070' -p1514 -aS'VOG11071' -p1515 -aS'VOG11075' -p1516 -aS'VOG11080' -p1517 -aS'VOG11081' -p1518 -atp1519 -bsg36 -Nstp1520 -Rp1521 -a(lp1522 -g19 -(g20 -(I0 -tp1523 -g22 -tp1524 -Rp1525 -(I1 -(I2 -I1474 -tp1526 -g29 -I00 -(lp1527 -S'V protein' -p1528 -aS'major coat protein' -p1529 -aS'phage assembly protein' -p1530 -aS'Vpf491' -p1531 -aS'putative minor coat protein' -p1532 -aS'putative transcription regulator' -p1533 -aS'DNA replication initiation protein' -p1534 -aS'putative major coat protein' -p1535 -aS'S-adenosyl-L-methionine hydrolase' -p1536 -aS'DNA ligase' -p1537 -aS'RNA polymerase' -p1538 -aS'putative DNA helicase' -p1539 -aS'DNA polymerase' -p1540 -aS'exonuclease' -p1541 -aS'head-tail connector protein' -p1542 -aS'capsid assembly protein' -p1543 -aS'tail tubular protein B' -p1544 -aS'internal virion protein A' -p1545 -aS'internal virion protein C' -p1546 -aS'internal virion protein D' -p1547 -aS'type II holin' -p1548 -aS'superinfection exclusion protein' -p1549 -aS'RtcB' -p1550 -aS'dCMP deaminase' -p1551 -aS'terminase large subunit' -p1552 -aS'RNA polymerase sigma factor' -p1553 -aS'holin' -p1554 -aS'P-starvation inducible protein' -p1555 -aS'major capsid protein' -p1556 -aS'tail sheath protein' -p1557 -aS'recombination endonuclease subunit' -p1558 -aS"deoxyuridine 5'-triphosphate nucleotidohydrolase" -p1559 -aS'ribonucleotide reductase' -p1560 -aS'thymidylate synthase' -p1561 -ag1552 -ag1554 -aS'serine/threonine protein phosphatase' -p1562 -aS'maturation protein' -p1563 -aS'replicase' -p1564 -aS'gpA' -p1565 -aS'gpA*' -p1566 -aS'gpB' -p1567 -aS'gpK' -p1568 -aS'gpC' -p1569 -aS'gpD' -p1570 -aS'gpE' -p1571 -aS'gpJ' -p1572 -aS'gpF' -p1573 -aS'gpG' -p1574 -aS'gpH' -p1575 -ag1533 -aS'DNA replication protein' -p1576 -aS'putative head-tail joining protein' -p1577 -ag1577 -aS'putative tail component protein' -p1578 -aS'integrase' -p1579 -aS'tail fiber assembly protein' -p1580 -aS'ParB' -p1581 -aS'Gp63' -p1582 -aS'LysC' -p1583 -aS'Doc' -p1584 -aS'terminase small subunit' -p1585 -aS'portal protein' -p1586 -aS'DNA stabilization protein' -p1587 -ag1587 -aS'head assembly protein' -p1588 -aS'DNA transfer protein' -p1589 -ag1589 -aS'O-antigen conversion protein C' -p1590 -aS'GtrB' -p1591 -ag1579 -aS'Abc2 protein' -p1592 -aS'Arf' -p1593 -aS'Kil' -p1594 -aS'CIII protein' -p1595 -aS'SieB' -p1596 -aS'antitermination protein N' -p1597 -aS'NinB protein' -p1598 -aS'NinE protein' -p1599 -aS'NinF protein' -p1600 -aS'NinG protein' -p1601 -aS'late gene regulator Q' -p1602 -aS'endopeptidase' -p1603 -aS'Rz1 protein' -p1604 -aS'Gp18 protein' -p1605 -aS'Gp45 protein' -p1606 -ag1540 -aS'putative DNA-packaging protein' -p1607 -aS'nicotinamide phosphoribosyltransferase' -p1608 -aS'prohead core scaffolding protein and protease' -p1609 -aS'replication protein P' -p1610 -ag1557 -aS'NAD-dependent DNA ligase subunit A' -p1611 -aS'DNA helicase' -p1612 -aS'DNA topoisomerase II large subunit' -p1613 -aS'DNA topisomerase II medium subunit' -p1614 -aS'ADP-ribosylase' -p1615 -aS'dUTPase' -p1616 -aS'spackle periplasmic protein' -p1617 -aS'head vertex assembly chaperone' -p1618 -aS'clamp loader subunit' -p1619 -aS'sliding clamp DNA polymerase accessory protein' -p1620 -aS'RNA polymerase binding protein' -p1621 -aS'alpha-glucosyl-transferase' -p1622 -aS'anaerobic NTP reductase small subunit' -p1623 -aS'anaerobic NTP reductase large subunit' -p1624 -aS'inhibitor of host Lon protease' -p1625 -aS'site-specific RNA endonuclease' -p1626 -aS'nudix hydrolase' -p1627 -aS'head completion protein' -p1628 -aS'baseplate wedge subunit' -p1629 -ag1629 -aS'baseplate wedge subunit and tail pin' -p1630 -ag1630 -aS'fibritin' -p1631 -aS'neck protein' -p1632 -ag1632 -aS'tail sheath stabilizer and completion protein' -p1633 -aS'prohead core protein' -p1634 -ag1634 -aS'scaffold prohead core protein' -p1635 -ag1556 -aS'inhibitor of prohead protease' -p1636 -aS'UvsY' -p1637 -aS'baseplate hub subunit' -p1638 -aS'baseplate hub distal subunit' -p1639 -aS'baseplate hub subunit tail length determinator' -p1640 -aS'baseplate tail tube cap' -p1641 -aS'ADP-ribosyltransferase' -p1642 -aS'lysis inhibition accessory protein' -p1643 -aS'endonuclease II' -p1644 -aS'dihydrofolate reductase' -p1645 -aS'single-stranded DNA binding protein' -p1646 -aS'holin lysis mediator' -p1647 -aS'activator of middle period transcription' -p1648 -aS'nucleoid disruption protein' -p1649 -aS'Na/K ATPase' -p1650 -aS'Panton-Valentine leukocidin chain S precursor' -p1651 -aS'Panton-Valentine leukocidin chain F precursor' -p1652 -aS'transcriptional activator RinB' -p1653 -aS'capsid-scaffolding protein' -p1654 -aS'terminase endonuclease subunit' -p1655 -aS'head completion-stabilization protein' -p1656 -aS'tail synthesis protein X' -p1657 -aS'tail protein' -p1658 -aS'tail formation protein I' -p1659 -aS'major tail tube protein' -p1660 -ag1658 -aS'replication protein A' -p1661 -ag1554 -ag1572 -aS'scaffolding protein' -p1662 -ag1585 -aS'lysin' -p1663 -ag1554 -aS'DNA encapsidation protein' -p1664 -ag1554 -aS'lower collar protein' -p1665 -aS'major head protein' -p1666 -aS'upper collar protein' -p1667 -ag1658 -aS'putative minor structural protein' -p1668 -aS'putative DNA polymerase I' -p1669 -aS'RNA ligase' -p1670 -ag1568 -ag1586 -aS'minor capsid protein' -p1671 -ag1556 -aS'putative minor capsid protein' -p1672 -ag1672 -ag1554 -aS'FtsK/SpoIIIE protein' -p1673 -aS'conserved phage protein' -p1674 -ag1586 -ag1554 -aS'putative topoisomerase' -p1675 -aS'Rad52/22 family double-strand break repair protein' -p1676 -aS'capsid protein' -p1677 -ag1554 -aS'excisionase' -p1678 -ag1585 -aS'major tail protein' -p1679 -aS'head-tail adaptor' -p1680 -ag1678 -aS'mobile element protein' -p1681 -aS'putative single-stranded DNA binding protein' -p1682 -aS'Bor protein precursor' -p1683 -aS'terminase small subunit nu1' -p1684 -aS'head-to-tail joining protein' -p1685 -ag1586 -aS'head-DNA stabilization protein' -p1686 -aS'DNA packaging protein' -p1687 -aS'head-tail connector Fii' -p1688 -aS'minor tail protein' -p1689 -aS'minor tail protein U' -p1690 -aS'minor tail protein G' -p1691 -ag1689 -ag1689 -ag1689 -ag1658 -aS'attachment invasion locus protein precursor' -p1692 -aS'terminal protein' -p1693 -aS'transcriptional regulator' -p1694 -aS'single stranded DNA-binding protein' -p1695 -aS'dsDNA binding protein' -p1696 -ag1662 -aS'head fiber protein' -p1697 -aS'DNA replication organizer' -p1698 -aS'putative protein 16.8' -p1699 -aS'putative terminase small subunit' -p1700 -aS'putative strucural protein 2' -p1701 -aS'putative strucural protein 4' -p1702 -ag1554 -aS'putative sak protein' -p1703 -aS'putative structural protein' -p1704 -aS'putative DNA polymerase subunit' -p1705 -aS'putative strucural protein 3' -p1706 -aS'neck passage structure' -p1707 -aS'transposase' -p1708 -ag1681 -aS'shiga-like toxin II subunit A precursor' -p1709 -aS'Shiga toxin 2 subunit B' -p1710 -aS'Putative small subunit (Nu1 homolog) of DNA packaging dimer' -p1711 -ag1556 -aS'retron-type RNA-directed DNA polymerase' -p1712 -aS'ParA' -p1713 -aS'protelomerase' -p1714 -aS'gp55 protein' -p1715 -aS'putative endolysin' -p1716 -ag1619 -ag1638 -aS'queuosine biosynthesis QueE radical SAM' -p1717 -aS'portal vertex protein' -p1718 -aS'tail tube protein' -p1719 -aS'sigma factor for late transcription' -p1720 -aS'QueC' -p1721 -ag1708 -aS'thymidine kinase' -p1722 -aS'nucleotide-sugar epimerase' -p1723 -aS'gp4' -p1724 -aS'putative co-chaperonin GroES' -p1725 -aS'putative HTH transcription regulator' -p1726 -aS'UDP-galactopyranose mutase' -p1727 -aS'EPS-depolymerase' -p1728 -ag1585 -ag1556 -aS'major tail subunit' -p1729 -ag1689 -ag1689 -aS'RNaseE' -p1730 -ag1689 -ag1689 -ag1689 -aS'gp81' -p1731 -aS'gp40' -p1732 -ag1586 -ag1556 -aS'DNA polymerase III alpha subunit' -p1733 -aS'galactosyltransferase' -p1734 -aS'glycosyltransferase' -p1735 -aS'tail assembly chaperone' -p1736 -ag1689 -ag1554 -aS'Lsr2' -p1737 -aS'gp13' -p1738 -aS'predicted hydrolase' -p1739 -aS'CHC2 zinc finger protein' -p1740 -aS'conserved hypothetical protein' -p1741 -aS'putative methyltransferase' -p1742 -ag1741 -aS'RecT' -p1743 -aS'PcfU' -p1744 -ag1741 -ag1666 -ag1556 -aS'HNH endonuclease' -p1745 -aS'nicotinamide mononucleotide transporter' -p1746 -aS'putative Sir2-like protein' -p1747 -aS'transaldolase-like protein' -p1748 -aS'DUF680 domain-containing protein' -p1749 -aS'photosystem II D1 protein' -p1750 -aS'high light inducible protein' -p1751 -aS'tail fiber protein' -p1752 -ag1700 -aS'putative tail protein' -p1753 -ag1736 -ag1689 -aS'DNA primase' -p1754 -aS'gp63' -p1755 -aS'gp80' -p1756 -aS'gp75' -p1757 -ag1581 -aS'esterase/lipase' -p1758 -aS'translation repressor' -p1759 -aS'base plate hub assembly catalyst' -p1760 -aS'head assembly cochaperone with GroEL' -p1761 -aS'tRNA nucleotidyltransferase' -p1762 -aS'loader of DNA helicase' -p1763 -aS'late promoter transcription accessory protein' -p1764 -aS'anti-sigma 70 protein' -p1765 -aS'NudE nudix hydrolase' -p1766 -aS'gp35 hinge long tail fiber proximal connector' -p1767 -ag1738 -aS'putative terminase large subunit' -p1768 -ag1556 -ag1554 -aS'cell adhesion domain-containing protein' -p1769 -aS'putative portal protein' -p1770 -aS'AAA ATPase' -p1771 -aS'small outer capsid protein' -p1772 -aS'internal head protein' -p1773 -aS'homing endonuclease' -p1774 -aS'hinge connector of long tail fiber proximal connector' -p1775 -aS'DNA endonuclease IV' -p1776 -aS'gp5' -p1777 -aS'gp8' -p1778 -aS'gp3' -p1779 -aS'phosphoribosyl transferase' -p1780 -ag1585 -aS'Cor protein' -p1781 -aS'serine/threonine kinase' -p1782 -ag1687 -aS'putative major tail protein' -p1783 -aS'methyltransferase' -p1784 -aS'Ren protein' -p1785 -aS'major tropism determinant' -p1786 -aS'transposase A' -p1787 -aS'acridine resistance protein' -p1788 -aS'putative tail tube protein' -p1789 -aS'putative tail sheath protein' -p1790 -aS'CI' -p1791 -ag1554 -aS'Apl' -p1792 -ag1671 -aS'replication protein VP4' -p1793 -aS'major capsid protein VP1' -p1794 -aS'internal scaffolding protein VP3' -p1795 -aS'protein kinase' -p1796 -aS'host dGTPase inhibitor' -p1797 -aS'gp1.5' -p1798 -aS'host RNA polymerase inhibitor' -p1799 -ag1745 -aS'guanylate kinase' -p1800 -aS'ribonucleoside triphosphate reductase, alpha chain' -p1801 -aS'virion RNA polymerase' -p1802 -ag1529 -ag1586 -ag1695 -aS'phage lambda Rz1-like protein' -p1803 -aS'valyl-tRNA synthetase modifier' -p1804 -aS'transcription modulator' -p1805 -aS'distal long tail fiber assembly catalyst' -p1806 -aS'IpI' -p1807 -ag1779 -ag1736 -ag1689 -ag1554 -aS'antirestriction protein' -p1808 -aS'gp1' -p1809 -ag1585 -ag1736 -aS'gp28' -p1810 -aS'gp31' -p1811 -aS'metallophosphoesterase' -p1812 -aS'gp2' -p1813 -aS'gp9' -p1814 -aS'gp16' -p1815 -aS'gp24' -p1816 -ag1736 -ag1810 -aS'gp33' -p1817 -aS'gp34' -p1818 -ag1809 -aS'gp59' -p1819 -ag1813 -ag1554 -aS'HTH DNA binding protein' -p1820 -aS'GIY-YIG endonuclease' -p1821 -ag1820 -aS'gp96' -p1822 -aS'putative holin' -p1823 -aS'putative transcriptional regulator' -p1824 -aS'putative DNA primase' -p1825 -aS'Ner-like protein' -p1826 -aS'DNA transposition protein' -p1827 -ag1557 -aS'tail/DNA circulation protein' -p1828 -ag1658 -aS'putative head protein' -p1829 -aS'Ser/Thr kinase' -p1830 -ag1735 -aS'gp18' -p1831 -aS'gp21' -p1832 -aS'LipC' -p1833 -aS'AddA-like protein' -p1834 -aS'gp205' -p1835 -aS'Ku protein' -p1836 -ag1724 -aS'gp7' -p1837 -aS'gp78' -p1838 -aS'gp56' -p1839 -aS'RDF protein' -p1840 -aS'gp82' -p1841 -aS'gp85' -p1842 -aS'gp86' -p1843 -ag1585 -aS'enoyl-CoA-hydratase' -p1844 -ag1784 -aS'gp19' -p1845 -aS'gp91' -p1846 -aS'gp94' -p1847 -aS'gp148' -p1848 -aS'gp131' -p1849 -ag1835 -ag1777 -aS'phosphoesterase' -p1850 -aS'tyrosine phosphatase' -p1851 -aS'gp37' -p1852 -ag1724 -aS'gp67' -p1853 -ag1809 -ag1779 -aS'gp139' -p1854 -aS'RecA' -p1855 -aS'ATP-dependent helicase' -p1856 -ag1556 -aS'maturation/adhesion protein' -p1857 -ag1841 -ag1831 -aS'gp22' -p1858 -aS'gp29' -p1859 -aS'gp30' -p1860 -aS'gp15' -p1861 -aS'FtsK-like protein' -p1862 -aS'gp90' -p1863 -aS'GTP cyclohydrolase I' -p1864 -aS'putative tail fiber' -p1865 -aS'phosphatidylglycerophosphatase A' -p1866 -aS'IMP dehydrogenase/GMP reductase' -p1867 -aS'small acid-soluble spore protein' -p1868 -ag1539 -aS'Ser/Thr protein phosphatase family protein' -p1869 -aS'putative UV damage repair endonuclease' -p1870 -aS'virion structural protein' -p1871 -ag1871 -aS'putative helicase' -p1872 -ag1556 -ag1871 -ag1871 -ag1790 -aS'putative virion structural protein' -p1873 -ag1873 -aS'addiction module toxin, RelE/StbE family' -p1874 -aS'Vpf76' -p1875 -aS'activator of host PrrC lysyl-tRNA endonuclease' -p1876 -aS'putative excisionase' -p1877 -aS'minor coat protein' -p1878 -ag1579 -aS'putative HTH transcriptional regulator' -p1879 -aS'helix-turn-helix protein' -p1880 -aS'structural protein V1' -p1881 -aS'structural protein VP3' -p1882 -aS'VP2-like protein' -p1883 -aS'NinD' -p1884 -aS'host recBCD nuclease inhibitor' -p1885 -aS'Cox' -p1886 -aS'Hol' -p1887 -aS'nonstructural protein' -p1888 -aS'Gp29' -p1889 -ag1817 -aS'gp42 protein' -p1890 -aS'transcription antiterminator' -p1891 -aS'gp51' -p1892 -ag1689 -ag1779 -aS'gp4a' -p1893 -ag1777 -aS'gp12' -p1894 -ag1729 -aS'GtrA' -p1895 -aS'NinY' -p1896 -aS'O-polysaccharide acetyltransferase protein' -p1897 -ag1533 -ag1678 -aS'CRISPR-associated Cas4-like protein' -p1898 -ag1872 -aS'DNA binding protein' -p1899 -aS'putative regulatory protein' -p1900 -ag1900 -aS'structural protein' -p1901 -ag1901 -aS'putative glycosyltransferase' -p1902 -aS'gp32' -p1903 -ag1732 -aS'gp46' -p1904 -aS'exfoliative toxin A' -p1905 -aS'gp8, conserved hypothetical protein' -p1906 -aS'gp71' -p1907 -aS'gp17' -p1908 -aS'gp26, bacteriophage lysis protein' -p1909 -aS'gp27' -p1910 -ag1859 -ag1860 -ag1811 -aS'gp32, hypothetical protein' -p1911 -aS'gp45, hypothetical protein' -p1912 -ag1755 -aS'putative chromosome partitioning protein' -p1913 -aS'gp62' -p1914 -ag1724 -aS'gp65' -p1915 -aS'gp43, conserved domain protein' -p1916 -aS'putative integral membrane protein' -p1917 -aS'putative transposase' -p1918 -ag1658 -aS'putative protease' -p1919 -ag1845 -aS'BcepNY3gp56' -p1920 -ag1914 -ag1662 -ag1666 -ag1678 -aS'77ORF046' -p1921 -ag1871 -aS'thymidylate kinase' -p1922 -aS'putative SNF2 domain helicase' -p1923 -aS'putative endoprotease' -p1924 -ag1556 -aS"Rz1 gp24'" -p1925 -aS'p11' -p1926 -aS'p53' -p1927 -aS'putative internal virion protein A' -p1928 -ag1540 -aS'putative glutathionylspermidine synthase' -p1929 -aS'gp40, hypothetical protein' -p1930 -ag1790 -ag1813 -ag1755 -aS'A2 protein' -p1931 -aS'D2 protein' -p1932 -aS'D3 protein' -p1933 -aS'D5 protein' -p1934 -aS'tail protein Pb4' -p1935 -ag1658 -aS'pore-forming tail tip protein' -p1936 -ag1689 -aS'putative transposase A subunit' -p1937 -aS'gp35' -p1938 -aS'2OG-Fe(II) oxygenase' -p1939 -ag1901 -ag1871 -aS'tail fiber-like protein' -p1940 -aS'methylamine protein' -p1941 -aS'peptidase' -p1942 -aS'heat shock protein' -p1943 -ag1871 -aS'photosystem II D2 protein' -p1944 -aS'S-adenosylmethionine decarboxylase' -p1945 -aS'antenna protein' -p1946 -ag1939 -aS'ferrochelatase' -p1947 -aS'tryptophan halogenase' -p1948 -aS'phycoerythrobilin' -p1949 -aS'CP12 protein' -p1950 -aS'baseplate wedge initiator' -p1951 -aS'DNA endonuclease V' -p1952 -aS'5-phosphoribosylformylglycinamide amidotransferase' -p1953 -aS'phosphoribosylaminoimidazole synthetase' -p1954 -ag1954 -aS'cytitidyltransferase' -p1955 -aS'plasmid stability protein' -p1956 -aS'plastocyanine' -p1957 -aS'phosphate transporter subunit' -p1958 -aS'glycosyltransferase family 11' -p1959 -aS'glycosyltransferase family 25' -p1960 -aS'ferredoxin' -p1961 -aS'heme oxygenase' -p1962 -aS'carbamoyltransferase' -p1963 -aS'putative nucleotidyltransferase' -p1964 -aS'putative carbohydrate kinase' -p1965 -ag1964 -aS'cAMP phosphodiesterase' -p1966 -ag1901 -aS'putative short tail fiber' -p1967 -aS'hemagglutinin domain-containing protein' -p1968 -ag1901 -aS'plastoquinol terminal oxidase' -p1969 -aS'S-layer domain protein' -p1970 -aS'carboxylesterase' -p1971 -aS'putative major capsid protein' -p1972 -ag1813 -aS'putative membrane protein' -p1973 -ag1708 -ag1918 -aS'6-phosphogluconate dehydrogenase' -p1974 -aS'glucose 6-phosphate dehydrogenase' -p1975 -aS'DUF1583 domain-containing protein' -p1976 -aS'putative phosphatase' -p1977 -aS'putative bacterial NUDIX hydrolase' -p1978 -aS'phosphoribosylaminoimidazole-succinocarboxamide synthase' -p1979 -aS'PA14 domain-containing protein' -p1980 -aS'RNA-dependent RNA polymerase' -p1981 -ag1552 -aS'tape measure protein' -p1982 -aS'lysin A' -p1983 -aS'helicase' -p1984 -aS'glutaredoxin' -p1985 -ag1754 -ag1556 -ag1662 -ag1586 -ag1729 -ag1689 -aS'lysin B' -p1986 -ag1561 -aS'ribonucleotide reductase subunit B' -p1987 -aS'lysozyme' -p1988 -aS'DNA methylase' -p1989 -ag1689 -ag1989 -ag1556 -ag1983 -ag1558 -ag1540 -ag1736 -aS'WhiB' -p1990 -aS'baseplate hub subunit and tail lysozyme' -p1991 -ag1679 -aS'D-ala-D-ala carboxypeptidase' -p1992 -aS'baseplate wedge tail fiber connector' -p1993 -aS'tail tubular protein A' -p1994 -aS'protector from prophage-induced early lysis' -p1995 -aS'DNA end protector protein' -p1996 -ag1752 -aS'minor structural protein' -p1997 -ag1541 -ag1556 -ag1904 -ag1586 -ag1754 -aS'replicative helicase' -p1998 -aS'internal virion protein B' -p1999 -aS'putative tail lysin' -p2000 -ag1809 -aS'hinge connector of long tail fiber distal connector' -p2001 -ag1735 -ag1658 -ag1729 -ag1736 -aS'tailspike protein' -p2002 -aS'capsid maturation protease' -p2003 -aS'baseplate J' -p2004 -aS'LysB' -p2005 -aS'putative tail fiber protein' -p2006 -aS'putative helicase-primase' -p2007 -ag1663 -ag1579 -aS'virion morphogenesis protein' -p2008 -ag1991 -ag1989 -aS'putative antireceptor' -p2009 -aS'pre-neck appendage protein' -p2010 -aS'putative replication origin binding protein' -p2011 -ag1859 -ag1983 -aS'assembly protein' -p2012 -aS'tailspike 63D sialidase' -p2013 -aS'head maturation protease' -p2014 -ag1674 -ag1990 -aS'putative poly A polymerase' -p2015 -aS'glycosyltransferase/methyl transferase' -p2016 -ag1858 -ag1901 -aS'morphogenesis protein' -p2017 -aS'gp54' -p2018 -ag1694 -ag1541 -ag1629 -ag1585 -aS'tail completion and sheath stabilizer protein' -p2019 -ag1670 -aS'tail assembly protein' -p2020 -ag1629 -ag1716 -aS'RecE' -p2021 -ag1556 -aS'inhibitor of host transcription' -p2022 -aS'ribonuclease H' -p2023 -aS'baseplate wedge protein' -p2024 -aS'modifier of suppressor tRNAs' -p2025 -aS'gp6' -p2026 -aS'flavodoxin' -p2027 -ag1989 -ag1658 -ag1658 -aS'Kil protein' -p2028 -aS'glycosyl transferase' -p2029 -ag1689 -ag1689 -aS'peptidase_S74 domain protein' -p2030 -ag1585 -aS'N-acetylmuramoyl-L-alanine amidase' -p2031 -aS'capsid portal protein Q' -p2032 -aS'gp11' -p2033 -aS'histidine triad domain protein' -p2034 -aS'DNA delivery' -p2035 -ag1753 -ag1679 -aS'endolysin' -p2036 -aS'O-methyltransferase' -p2037 -aS'putative ribonuclease H' -p2038 -aS'NAD-dependent DNA ligase' -p2039 -aS'modifier of transcription' -p2040 -aS'tapemeasure' -p2041 -aS'DNA packaging ATPase' -p2042 -aS'gp74' -p2043 -ag1658 -aS'Hoc large outer capsid protein' -p2044 -ag1774 -aS'putative baseplate wedge protein' -p2045 -aS'long tail fiber distal subunit' -p2046 -aS'gp142' -p2047 -ag1811 -ag1990 -ag1738 -ag1700 -ag1663 -ag1877 -aS'recombinase' -p2048 -aS'internal (core) protein' -p2049 -aS'LysM domain-containing protein' -p2050 -aS'tailspike' -p2051 -aS'DR0530-like primase' -p2052 -aS'distal tail protein' -p2053 -aS'late control D protein' -p2054 -ag1658 -aS'putative peptidase M23' -p2055 -ag1823 -aS'Uncharacterized protein MJ0770' -p2056 -aS'ATPase family protein' -p2057 -aS'lytic protein Rz1' -p2058 -ag1871 -aS'HTH DNA binding domain protein' -p2059 -aS'Vs valyl-tRNA synthetase modifier' -p2060 -ag1668 -ag1938 -ag1754 -aS'glycerophosphoryl diesterphosphodiesterase' -p2061 -ag1586 -aS'putative site-specific intron-like DNA endonuclease' -p2062 -ag2020 -aS'head morphogeneis protein' -p2063 -ag1663 -aS'virion-associated phage protein' -p2064 -aS'CHAP domain protein' -p2065 -aS'DarB-like antirestriction protein' -p2066 -aS'replication protein' -p2067 -aS'partition protein ParB' -p2068 -aS'putative gp37' -p2069 -aS'gp10' -p2070 -ag1738 -ag1824 -aS'DarB' -p2071 -aS'Ant1' -p2072 -aS'gp41, hypothetical protein' -p2073 -aS'gp43' -p2074 -ag1918 -aS'putative phage repressor' -p2075 -aS'cytosine-specific DNA methyltransferase' -p2076 -aS'gp61' -p2077 -aS'gp23' -p2078 -ag1817 -aS'tail fiber' -p2079 -ag2070 -aS'phage terminase large subunit' -p2080 -aS'putative endonuclease' -p2081 -aS'gp50' -p2082 -ag1989 -aS'gp20' -p2083 -aS'putative bifunctional DNA primase/polymerase' -p2084 -ag1736 -aS'metal-dependent hydrolase' -p2085 -ag1724 -aS'Ro protein' -p2086 -aS'putative DNA-PolB associated exonuclease' -p2087 -ag1865 -ag2041 -ag1835 -aS'HNH endonuclease domain protein' -p2088 -ag1901 -aS'membrane protein' -p2089 -ag1901 -aS'replicative clamp' -p2090 -ag1974 -aS'DNA polymerase III beta subunit' -p2091 -aS'restriction endonuclease' -p2092 -aS'TreO' -p2093 -aS'putative head stabilization/decoration protein' -p2094 -ag2079 -ag1752 -aS'replication terminator protein' -p2095 -ag2027 -aS'putative DNA methylase' -p2096 -aS'TreB' -p2097 -aS'putative peptidase' -p2098 -ag1554 -aS'neck passage structure protein' -p2099 -aS'transposase-like protein' -p2100 -aS'putative outer membrane protein' -p2101 -aS'colanic acid-degrading protein' -p2102 -ag2028 -aS'positive control sigma-like factor' -p2103 -aS'putative peptidyl-tRNA hydrolase' -p2104 -aS'TreA' -p2105 -ag1554 -ag1680 -aS'NAD-dependent DNA ligase subunit B' -p2106 -ag1752 -aS'pre-TMP frameshift protein' -p2107 -aS'RNAse H' -p2108 -aS'pre-tape measure frameshift protein G-T' -p2109 -aS'putative phage tail protein' -p2110 -ag1700 -ag1704 -ag1823 -aS'constituent protein' -p2111 -aS'major capsid & capsid maturation protease' -p2112 -aS'head-to-tail connector' -p2113 -ag1679 -ag1689 -ag1529 -ag2078 -aS'putative DNA primase/polymerase' -p2114 -ag1586 -aS'recombination protein U' -p2115 -aS'topoisomerase II large subunit' -p2116 -aS'beta glucosyl transferase' -p2117 -ag1901 -aS'VI protein' -p2118 -ag2059 -aS'putative DNA N6-adenine methyltransferase' -p2119 -ag1831 -aS'rare lipoprotein A' -p2120 -ag1900 -aS'putative phage DNA primase' -p2121 -ag1901 -ag1771 -aS'pectate lyase' -p2122 -ag1541 -ag1901 -ag2041 -aS'gp26' -p2123 -ag1852 -ag1915 -aS'putative cell division control protein' -p2124 -aS'receptor-binding tail protein' -p2125 -ag1967 -ag1967 -aS'putative minor structural protein 1' -p2126 -aS'putative lower collar protein' -p2127 -aS'putative cell wall hydrolase protein' -p2128 -aS'carboxypeptidase A' -p2129 -aS'putative primase' -p2130 -aS'putative DNA replication protein' -p2131 -ag1658 -ag2048 -ag1773 -aS'phospho-2-dehydro-3-deoxyheptonate aldolase' -p2132 -ag1774 -aS'MazG' -p2133 -aS'prohead protease' -p2134 -aS'Appr-1-p processing protein' -p2135 -ag2006 -aS'putative encapsidation protein' -p2136 -aS'DNA pilot protein VP2' -p2137 -aS'putative DHH phosphoesterase protein' -p2138 -aS'HTH binding protein' -p2139 -ag1658 -aS'putative pre-tape measure chaperone protein' -p2140 -aS'putative tape measure protein' -p2141 -aS'tail lysozyme' -p2142 -aS'complement inhibitor' -p2143 -ag1989 -ag1716 -aS'coat protein' -p2144 -aS'VP4 precursor' -p2145 -aS'DnaA protein' -p2146 -aS'receptor-blocking protein' -p2147 -ag1556 -ag1784 -ag1704 -aS'antioxidant protein' -p2148 -aS'putative sporulation protein YhbH' -p2149 -aS'putative IS transposase (OrfA)' -p2150 -aS'putative DNA injection protein' -p2151 -ag2003 -ag1700 -aS'receptor-binding protein' -p2152 -aS'cell wall peptidase' -p2153 -ag1586 -aS'major capsid subunit' -p2154 -ag1552 -aS'LysM' -p2155 -ag1689 -ag1674 -ag1662 -aS'DNA polymerase IV' -p2156 -aS'abortive infection bacteriophage resistance protein' -p2157 -aS'pyruvate kinase' -p2158 -aS'peptide deformylase' -p2159 -ag1567 -ag1871 -aS'Rz' -p2160 -ag1694 -ag1552 -aS'chaperonin GroEL' -p2161 -ag2021 -ag1629 -ag2033 -aS'putative adsorption protein' -p2162 -ag1988 -aS'von Willebrand factor domain protein' -p2163 -ag1823 -aS'EaC protein' -p2164 -ag2006 -aS'putative DNAse/helicase protein' -p2165 -aS'LAGLIDADG endonuclease' -p2166 -aS'AbrB family transcriptional regulator' -p2167 -aS'putative transcriptional activator' -p2168 -ag1753 -ag1820 -ag1754 -aS'cell wall hydrolase' -p2169 -ag1997 -ag1754 -aS'tail connector protein' -p2170 -aS'PE/PPE-like protein' -p2171 -aS'acetyltransferase' -p2172 -aS'bacteriocin biosynthesis protein' -p2173 -aS'putative rIIa-like protein' -p2174 -aS'putative DNA polymerase' -p2175 -aS'Cro-like protein' -p2176 -aS'gp42' -p2177 -aS'lytic protein Rz' -p2178 -aS'DNA polymerase III subunit beta' -p2179 -aS'LysA' -p2180 -aS'putative 2-component regulator' -p2181 -aS'QueF' -p2182 -ag1824 -aS'transposase InsH, IS5D, IS5 family' -p2183 -aS'CRO protein' -p2184 -aS'YolD-like protein' -p2185 -aS'putative glucose-1-phosphate thymidylyltransferase' -p2186 -aS'putative base plate lysozyme' -p2187 -aS'adhesin' -p2188 -ag1901 -aS'chaperonin cpn10' -p2189 -ag1901 -ag1901 -ag1901 -ag1901 -ag1901 -ag2051 -ag1540 -aS'phage tail fiber protein' -p2190 -aS'HicA-like protein' -p2191 -ag1824 -aS'gene transfer agent' -p2192 -ag1689 -aS'MutT/NUDIX hydrolase family protein' -p2193 -ag1823 -aS'bacterial surface protein' -p2194 -aS'RNA polymerase ECF sigma factor' -p2195 -ag1780 -ag1736 -aS'phage tail protein' -p2196 -ag1752 -aS'Tail fiber protein' -p2197 -ag1754 -aS'putative IS transposase (OrfB)' -p2198 -aS'putative transglutaminase-like cysteine peptidase' -p2199 -ag1672 -aS'putative lectin-like domain protein' -p2200 -ag1753 -ag1753 -aS'putative holin protein' -p2201 -aS'putative inner membrane spanin component' -p2202 -aS'putative outer membrane spanin component' -p2203 -aS'putative HTH domain protein' -p2204 -aS'putative TAT signal protein' -p2205 -ag1585 -aS'putative ArdC-like antirestriction protein' -p2206 -ag1901 -ag1901 -ag1586 -aS'tape measure' -p2207 -aS'potassium voltage-gated channel subfamily A member 1 protein' -p2208 -aS'putative small terminase subunit' -p2209 -ag1736 -ag1770 -aS'putative rIIb-like protein' -p2210 -aS'intein-containing putative terminase large subunit precursor' -p2211 -ag1638 -aS'putative HNH endonuclease inducing intron mobility' -p2212 -aS'phage head-tail joining protein' -p2213 -aS'RNA polymerase-ADP-ribosyltransferase Alt' -p2214 -ag1899 -aS'putative phage-related hydrogenase' -p2215 -ag1662 -ag1871 -aS'staphylokinase' -p2216 -aS'chemotaxis-inhibiting protein CHIPS' -p2217 -aS'TerB' -p2218 -aS'long tail fiber distal subunit adhesine' -p2219 -aS'putative ABC transporter ATP-binding protein' -p2220 -aS'ea59' -p2221 -ag2175 -aS'AlpA-like transcriptional regulator' -p2222 -ag1784 -aS'ATP-dependent metalloprotease' -p2223 -ag1753 -ag1556 -aS'putative amidotransferase' -p2224 -ag1585 -aS'tRNA (cmo5U34)-methyltransferase' -p2225 -aS'EaI protein' -p2226 -aS'RecA-like recombination protein' -p2227 -aS'glycosyltransferase-family protein' -p2228 -ag1845 -ag1871 -aS'cI-like putative transcriptional regulator' -p2229 -aS'phycobilisome degredation protein' -p2230 -aS'VP4' -p2231 -aS'putative phage structural protein' -p2232 -aS'putative HD domain protein' -p2233 -aS'type II restriction enzyme BsuBI' -p2234 -aS'modification methylase BsuBI' -p2235 -ag1873 -ag1892 -ag1811 -ag1901 -aS'RstB' -p2236 -aS'YomR-like protein' -p2237 -aS'RIIA-like protein' -p2238 -ag1865 -aS'conserved hypothetical protein (XkdN-like)' -p2239 -aS'tail sheath' -p2240 -aS'aerobic NDP reductase small subunit' -p2241 -aS'putative DNA segregation ATPase FtsK/SpoIIIE' -p2242 -aS'PemK-like protein' -p2243 -aS'tail spike protein' -p2244 -ag2070 -aS'gp25' -p2245 -ag1553 -aS'replication factor C small subunit' -p2246 -aS'Mu F-like capsid morphogenesis protein' -p2247 -ag1871 -ag1823 -aS'regulator of chromosome condensation RCC1' -p2248 -aS'putative lysozyme' -p2249 -ag1557 -aS'putative virion protein and lysozyme murein' -p2250 -ag1784 -aS'putative tail fiber protein 1' -p2251 -ag1556 -aS'VRR-NUC domain containing protein' -p2252 -ag1989 -ag1902 -ag1542 -aS'putative tail length tape measure protein' -p2253 -ag1901 -ag1901 -aS'head outer capsid protein' -p2254 -aS'gp165' -p2255 -aS'base plate lysozyme' -p2256 -ag1579 -ag2006 -ag1585 -ag1745 -aS'putative DNA endonuclease VII' -p2257 -aS'site specific recombinase, tyrosine' -p2258 -ag1553 -ag2196 -ag1529 -aS'LydD' -p2259 -aS'OdaA' -p2260 -aS'PmgA' -p2261 -aS'RepA' -p2262 -aS'ShtB' -p2263 -aS'putative S-adenosylmethionine synthetase' -p2264 -aS'putative envelope protein' -p2265 -ag1778 -ag2033 -ag1861 -ag1832 -ag2078 -aS'virion protein' -p2266 -ag1865 -aS'peptidase-like protein' -p2267 -ag1708 -aS'capsid and scaffold protein' -p2268 -aS'PblB-type protein' -p2269 -ag1671 -ag1553 -aS'transcription regulatory protein' -p2270 -aS'zinc-ribbon domain-containing protein' -p2271 -aS'internal virion protein' -p2272 -aS'PCNA protein' -p2273 -ag1871 -aS'RNA polymerase sigma-70 factor' -p2274 -ag2064 -ag1554 -aS'helix-turn-helix domain protein' -p2275 -ag1751 -aS'phosphohydrolase' -p2276 -ag1658 -aS'PfWMP3_27' -p2277 -ag1544 -ag1994 -aS'scaffold protein' -p2278 -aS'enterotoxin type A precursor' -p2279 -aS'160 kDa protein' -p2280 -ag1873 -ag2002 -ag1755 -ag1561 -aS'ribonucleotide diphosphate reductas alpha subunit' -p2281 -ag1901 -aS'NAD+ synthetase' -p2282 -aS'putative tail fiber adhesion protein' -p2283 -ag1585 -aS'putative ribosomal-protein-alanine N-acetyltransferase' -p2284 -ag2010 -aS'putative lysozyme-peptidase' -p2285 -aS'putative DNA modification methylase' -p2286 -aS'putative aminoacyl-tRNA hydrolase' -p2287 -ag1752 -aS'possible virion structural protein' -p2288 -ag1971 -aS'phenylalanyl-tRNA synthetase subunit beta' -p2289 -ag2189 -ag1901 -ag1901 -ag1901 -aS'NifU-like protein' -p2290 -ag1755 -aS'beta-glucanase' -p2291 -ag2177 -aS'gp101' -p2292 -ag1540 -aS'helix-turn-helix XRE-family of transcriptional regulators' -p2293 -ag1922 -aS'major tail protein extension' -p2294 -aS'pIII-CTX' -p2295 -ag1900 -ag1679 -aS'RecA-like recombinase' -p2296 -ag1871 -ag1888 -aS'HNH protein' -p2297 -ag1918 -aS'Gp40 protein' -p2298 -aS'Gp41 protein' -p2299 -aS'Gp7 protein' -p2300 -aS'putative dehalogenase hydrolase-like protein' -p2301 -aS'putative phosphoribosyltransferase-like domain protein' -p2302 -aS'putative dTDP-4-dehydrorhamnose 3,5-epimerase' -p2303 -ag1736 -aS'putative virion structural protein 19' -p2304 -ag2272 -aS"putative RNA 2'-phosphotransferase" -p2305 -aS'putative NAD+ diphosphatase' -p2306 -aS'primase/polymerase' -p2307 -aS'Cre' -p2308 -aS'portal vertex protein of head' -p2309 -aS'LydA' -p2310 -aS'Phd' -p2311 -ag2089 -aS'minor tail protein L' -p2312 -ag2005 -aS'putative DNA binding protein' -p2313 -ag1752 -aS'putative nicotinamide mononucleotide transporter' -p2314 -ag1753 -ag2207 -ag1752 -ag1901 -aS'deaminase' -p2315 -ag2134 -aS'middle expressed protein 4' -p2316 -aS'putative bacterial RNA polymerase inhibitor' -p2317 -aS'glycosidase' -p2318 -aS'EaD protein' -p2319 -ag1752 -aS'phage DNA end protector during packaging' -p2320 -ag2088 -ag1552 -ag1745 -ag1783 -aS'immunoglobulin I-set domain protein' -p2321 -ag1658 -aS'minor tail protein Z' -p2322 -ag1752 -ag1752 -aS'C8' -p2323 -aS'Mat' -p2324 -aS'putative protein Ulx' -p2325 -aS'Pro' -p2326 -aS'conserved protein of unknown function, DdrB' -p2327 -aS'Upf26.7' -p2328 -aS'DarA' -p2329 -aS'conserved protein of unknown function Hdf' -p2330 -aS'LydB' -p2331 -aS'gpR' -p2332 -ag1815 -aS'PmgB' -p2333 -aS'major tail tube protein TubB' -p2334 -aS'PmgC' -p2335 -aS'putative outer membrane lipoprotein' -p2336 -aS'Icd' -p2337 -aS'RepL' -p2338 -aS'Upf52.7' -p2339 -aS'upf54.2' -p2340 -aS'tail sheath protein Gp22' -p2341 -aS'Upf57.5' -p2342 -aS'Upf62.7' -p2343 -aS'conserved protein of unknown function UpfB' -p2344 -aS'Upf64.0' -p2345 -aS'Dbn' -p2346 -ag2026 -aS'Upf78.5' -p2347 -ag1837 -ag2245 -ag2123 -aS'PmgN' -p2348 -aS'putative morphogenetic protein PmgP' -p2349 -aS'HdmD' -p2350 -aS'PmgR' -p2351 -aS'Fdc' -p2352 -aS'Lpa' -p2353 -aS'PacA' -p2354 -aS'C1.100' -p2355 -aS'Coi' -p2356 -ag2185 -aS'ea8.5' -p2357 -aS'putative mitochondrial DNA polymerase gamma homologue' -p2358 -ag1825 -aS'DNA polymerase I-like flap endonuclease (FEN)' -p2359 -aS'IS1 transposase B' -p2360 -ag1532 -ag2043 -aS'gp87' -p2361 -aS'gp114' -p2362 -aS'gp135' -p2363 -ag1819 -ag1745 -ag2083 -ag1892 -aS'gp97' -p2364 -aS'lytic conversion lipoprotein precursor' -p2365 -aS'BofR' -p2366 -aS'head-tail connector' -p2367 -aS'nucleoid-associated protein' -p2368 -ag1901 -ag1901 -ag1554 -aS'putative lysin' -p2369 -ag2089 -aS'glycosyl transferase group I' -p2370 -ag1901 -ag2224 -aS'plasmid maintenance system killer HigB' -p2371 -ag1554 -ag2268 -aS'core encoded pilin' -p2372 -aS'accessory cholera enterotoxin' -p2373 -ag1552 -aS'tail protein P' -p2374 -aS'formamidopyrimidine-DNA glycosylase' -p2375 -aS'putative head-tail connector protein' -p2376 -aS'Conserved hypothetical' -p2377 -aS'lysophospholipase L1-related esterase' -p2378 -ag2036 -aS'acetyltransferase domain protein' -p2379 -ag2088 -aS'XRE family transcriptional regulator' -p2380 -aS'S-layer domain-containing protein' -p2381 -aS'Hypothetical-Protein ' -p2382 -aS'sulfotransferase' -p2383 -ag1777 -aS'gp69' -p2384 -aS'palmitoyltransferase' -p2385 -aS'Ea47 protein' -p2386 -aS'Ea31 protein' -p2387 -aS'putative excinuclease ABC' -p2388 -ag1878 -ag1852 -aS'gp38' -p2389 -aS'gp39' -p2390 -aS'gp41' -p2391 -aS'gp45' -p2392 -aS'gp47' -p2393 -ag1892 -aS'Phage repressor' -p2394 -ag1813 -ag1724 -ag1861 -ag1831 -ag1858 -ag2078 -ag2245 -ag1888 -aS'O-antigen beta polymerase' -p2395 -ag1824 -aS'ssDNA-binding' -p2396 -aS'putative repressor' -p2397 -ag2078 -ag1810 -aS'gp34.26' -p2398 -aS'gp34 protein' -p2399 -aS'gp03 protein' -p2400 -ag1871 -aS'putative Kelch-like ECH-associated protein' -p2401 -ag1871 -ag1871 -ag1871 -ag1871 -ag1871 -ag1871 -ag1871 -ag1871 -ag1871 -ag1871 -ag1871 -ag1871 -ag1871 -ag1871 -aS'putative nucleotidyltransferase protein' -p2402 -ag1819 -ag1859 -aS'putative Fe-S oxidoreductase' -p2403 -ag2033 -ag2382 -ag1940 -aS'PRGA-formyltransferase' -p2404 -aS'putative protein 2' -p2405 -aS'VP13' -p2406 -aS'VP2' -p2407 -aS'capsid protein VP5' -p2408 -aS'putative protein 31' -p2409 -aS'putative protein 33' -p2410 -aS'putative terminase large subunit-like protein' -p2411 -ag2389 -aS'C-terminal part of the MCM2-like helicase' -p2412 -ag2268 -ag1752 -aS'putative antirestriction protein' -p2413 -ag1865 -ag2020 -ag1951 -aS'putative topoisomerasae I protein' -p2414 -aS'putative ATPase' -p2415 -aS'trypsin-like serine protease domain protein' -p2416 -aS'gp14-like protein' -p2417 -aS'antirepressor' -p2418 -aS'gp18.5' -p2419 -ag1677 -aS'glycerophosphodiester phosphodiesterase' -p2420 -ag1629 -ag1754 -aS'putative quaternary ammonium compound-resistance protein qacE' -p2421 -aS'gp134' -p2422 -aS'Very-short-patch mismatch repair endonuclease' -p2423 -aS'putative cytoplasmic protein' -p2424 -aS'alkaline phosphatase' -p2425 -aS'putative DNA binding excisionase protein' -p2426 -aS'metallo-beta-lactamase domain-containing protein' -p2427 -aS'putative SpoVG protein' -p2428 -ag1552 -aS'CobS porphyrin biosynthetic protein' -p2429 -ag2006 -aS'Possible tail sheath protein' -p2430 -aS'Possible phage tail tube protein' -p2431 -aS'putative transketolase' -p2432 -aS'putative N-acetylneuraminate pyruvate lyase' -p2433 -aS'putative minor tail assembly protein' -p2434 -aS'putative UDP-glucose dehydrogenase' -p2435 -ag1823 -aS'HicB protein' -p2436 -ag1752 -aS'putative acetyltransferase' -p2437 -aS'putative radical SAM superfamily protein 2' -p2438 -aS'Hef nuclease' -p2439 -aS'replication factor C large subunit' -p2440 -aS'RadA' -p2441 -ag1586 -aS'gpF-like protein' -p2442 -aS'zeta toxin domain protein' -p2443 -ag1556 -ag1736 -aS'RNAse HI' -p2444 -ag1540 -ag1556 -ag1752 -aS'DUF3800 domain-containing protein' -p2445 -ag1901 -aS'VirE N-domain protein' -p2446 -aS'gp77' -p2447 -ag2130 -aS'prophage protein' -p2448 -aS'gp004' -p2449 -ag1756 -aS'gp241' -p2450 -ag1809 -aS'gp44' -p2451 -ag1938 -aS'tail tape measure chaperone protein' -p2452 -aS'BTLCP-like protein' -p2453 -ag1552 -aS'putative protein containing Nos-D like domain' -p2454 -aS'peptidase M15' -p2455 -aS'putative homing endonuclease' -p2456 -aS'elongation factor Ts-like protein' -p2457 -aS'S-adenosylmethionine decarboxylase-like protein' -p2458 -aS'putative peptidase-like protein' -p2459 -aS'signal peptide protein' -p2460 -aS'RelA/SpoT family protein' -p2461 -ag1585 -aS'DNA topoisomerase II large subunit C-terminal region' -p2462 -ag1858 -ag1671 -aS'putative Transcription initiation factor B' -p2463 -aS'packaging NTPase P4' -p2464 -ag1572 -aS'RNA ligase 2' -p2465 -ag1861 -ag2006 -aS'chaperone protein DnaK' -p2466 -aS'capsid decoration protein' -p2467 -aS'gp14' -p2468 -aS'prophage antirepressor' -p2469 -ag1938 -ag2046 -ag2224 -ag1878 -ag1845 -ag1997 -ag1554 -aS'o-spanin' -p2470 -ag2389 -ag1753 -ag1658 -ag1790 -ag2006 -aS'cytolethal distending toxin V B subunit' -p2471 -aS'minor structural protein gp58' -p2472 -aS'putative peptidase/serine protease' -p2473 -aS'DNA polymerase subunit III' -p2474 -aS'adenosylribosyltransferase' -p2475 -aS'peptidase domain-containing protein' -p2476 -aS'head morphogenesis protein' -p2477 -aS'putative TROVE-like domain protein' -p2478 -ag1824 -aS'putative radical SAM superfamily protein 1' -p2479 -ag1662 -ag1901 -ag1982 -aS'gp53 protein' -p2480 -ag1752 -ag2141 -aS'DNA-binding protein' -p2481 -aS'putative crossover junction endodeoxyribonuclease RusA' -p2482 -aS'Rec A-like recombinase' -p2483 -aS'Other' -p2484 -aS'Coat' -p2485 -aS'Assembly' -p2486 -ag2484 -ag2485 -ag2484 -aS'Replication' -p2487 -ag2485 -ag2484 -ag2487 -ag2484 -ag2487 -ag2487 -ag2484 -aS'Other (structural)' -p2488 -ag2486 -aS'Tail' -p2489 -ag2484 -ag2484 -ag2484 -aS'Lysis' -p2490 -ag2484 -ag2484 -ag2484 -aS'Terminase' -p2491 -ag2484 -ag2490 -ag2484 -ag2485 -ag2489 -ag2484 -ag2484 -ag2484 -ag2484 -ag2491 -ag2490 -ag2484 -ag2486 -ag2487 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2487 -ag2488 -ag2488 -ag2489 -aS'Integration' -p2492 -ag2486 -ag2484 -ag2484 -ag2484 -ag2484 -ag2491 -aS'Portal' -p2493 -ag2484 -ag2484 -ag2486 -ag2484 -ag2484 -ag2484 -ag2484 -ag2492 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2487 -ag2484 -ag2484 -ag2484 -ag2487 -ag2489 -ag2487 -ag2487 -ag2487 -ag2484 -ag2484 -ag2484 -ag2484 -ag2486 -ag2484 -ag2487 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2486 -aS'Baseplate' -p2494 -ag2494 -ag2489 -ag2489 -ag2484 -ag2484 -ag2484 -ag2486 -ag2484 -ag2484 -ag2484 -ag2485 -ag2484 -ag2484 -ag2494 -ag2494 -ag2489 -ag2489 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2490 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2491 -ag2486 -ag2489 -ag2489 -ag2486 -ag2489 -ag2489 -ag2487 -ag2490 -ag2484 -ag2484 -ag2491 -ag2490 -ag2490 -ag2486 -ag2490 -ag2484 -ag2484 -ag2484 -ag2489 -ag2484 -ag2487 -ag2484 -ag2484 -ag2493 -ag2485 -ag2485 -ag2485 -ag2485 -ag2490 -ag2484 -ag2484 -ag2493 -ag2490 -ag2487 -ag2484 -ag2485 -ag2490 -ag2484 -ag2491 -ag2489 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2491 -ag2488 -ag2493 -ag2484 -ag2484 -ag2488 -ag2489 -ag2489 -ag2489 -ag2489 -ag2489 -ag2489 -ag2489 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2487 -ag2484 -ag2491 -ag2484 -ag2484 -ag2490 -ag2484 -ag2484 -ag2487 -ag2484 -ag2484 -ag2492 -ag2484 -ag2484 -ag2484 -ag2484 -ag2485 -ag2484 -ag2484 -ag2484 -ag2484 -ag2490 -ag2484 -ag2494 -ag2484 -ag2493 -ag2489 -ag2484 -ag2484 -ag2492 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2487 -ag2491 -ag2485 -ag2489 -ag2489 -ag2489 -ag2484 -ag2489 -ag2489 -ag2489 -ag2484 -ag2484 -ag2493 -ag2485 -ag2487 -ag2484 -ag2484 -ag2486 -ag2489 -ag2490 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2485 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2489 -ag2491 -ag2489 -ag2486 -ag2489 -ag2487 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2484 -ag2486 -ag2486 -ag2484 -ag2487 -ag2484 -ag2484 -ag2484 -ag2488 -ag2484 -ag2491 -ag2485 -ag2490 -ag2484 -ag2493 -ag2484 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-git pull -echo "Recovering Windows-Linux issues" -C:\Users\tikho\Anaconda3\python.exe recover_pickle_files.py -pause -move /-Y dist\*.* dist_old_versions\ -C:\Users\tikho\Anaconda3\python.exe setup_version.py -pause -C:\Users\tikho\Anaconda3\python.exe setup.py sdist bdist_wheel -pause -git add --all -git status -pause -set /P commit_name="Please, make up the commit name:" -set /p tag==1.7.0', - 'pandas>=0.23.4', - 'sh', - 'singleton', - 'PyYAML>=5.1', - 'future', - 'argparse', - 'numpy', - 'plotly', - 'bs4', - 'beautifulsoup4>=4.4.0', - 'lxml', - 'biopython', + "numpy", + "six>=1.7.0", + "pandas>=0.23.4", + "sh", + "singleton", + "PyYAML>=5.1", + "future", + "argparse", + "numpy", + "plotly", + "bs4", + "beautifulsoup4>=4.4.0", + "lxml", + "biopython", ], ) diff --git a/setup_version.py b/setup_version.py index 7a4e468..f307f08 100644 --- a/setup_version.py +++ b/setup_version.py @@ -6,80 +6,78 @@ from copy import deepcopy -setup_file = 'setup.py' -version_file = 'phigaro/_version.py' -readme_file = 'README.md' -latest_version_file = 'test_data_gitaction/latest_version.txt' -tag_file = 'tag_name' +setup_file = "setup.py" +version_file = "phigaro/_version.py" +readme_file = "README.md" +latest_version_file = "test_data_gitaction/latest_version.txt" +tag_file = "tag_name" -with open(setup_file, 'r') as f: +with open(setup_file, "r") as f: tmp_version = f.readlines()[12].strip() -print('Temporary %s' % tmp_version) +print("Temporary %s" % tmp_version) -tmp_version = ( - tmp_version.replace('version=', '').replace('"', '').replace(',', '') -) -tmp_version = tmp_version.split('.') +tmp_version = tmp_version.replace("version=", "").replace('"', "").replace(",", "") +tmp_version = tmp_version.split(".") version_variants = [] for i in list(range(len(tmp_version)))[::-1]: tmp_version_ = deepcopy(tmp_version) tmp_version_[i] = str(int(tmp_version_[i]) + 1) - version_variants.append('.'.join(tmp_version_)) - tmp_version[i] = '0' + version_variants.append(".".join(tmp_version_)) + tmp_version[i] = "0" def ask_version(version_variants): def confirm(version, version_variants): - print('Do you agree? Yes/No') + print("Do you agree? Yes/No") user_answer = input() - if user_answer.upper() in {'Y', 'YES'}: + if user_answer.upper() in {"Y", "YES"}: return version - elif user_answer.upper() in {'N', 'NO'}: + elif user_answer.upper() in {"N", "NO"}: return ask_version(version_variants) else: confirm(version, version_variants) for i, version in enumerate(version_variants): - print('[%d] %s' % (i, version)) - print('[%d] Type your version' % (len(version_variants))) + print("[%d] %s" % (i, version)) + print("[%d] Type your version" % (len(version_variants))) user_answer = input() try: version = version_variants[int(user_answer)] except: version = user_answer print() - print('You choose version: %s' % version) + print("You choose version: %s" % version) return confirm(version, version_variants) version = ask_version(version_variants) for file_ in [setup_file, version_file]: - with open(file_, 'r') as f: + with open(file_, "r") as f: lines = f.readlines() lines_new = [] for line in lines: - if ('version="' in line) or ('__version__' in line): - line = '='.join(line.split('=')[:-1] + ['"%s",' % version]) - if '__version__' in line: + if ('version="' in line) or ("__version__" in line): + line = "=".join(line.split("=")[:-1] + ['"%s",' % version]) + if "__version__" in line: line = line[:-1] - line = line + '\n' + line = line + "\n" lines_new.append(line) - with open(file_, 'w') as f: - f.write(''.join(lines_new)) + with open(file_, "w") as f: + f.write("".join(lines_new)) -with open(readme_file, 'r') as f: +with open(readme_file, "r") as f: lines = f.readlines() -lines[0] = '# Phigaro v%s\n' % version -with open(readme_file, 'w') as f: - f.write(''.join(lines)) +lines[0] = "# Phigaro v%s\n" % version +with open(readme_file, "w") as f: + f.write("".join(lines)) -with open(latest_version_file, 'w') as f: +with open(latest_version_file, "w") as f: f.write( - 'https://github.com/bobeobibo/phigaro/raw/master/dist/phigaro-%s.tar.gz' + "https://github.com/bobeobibo/phigaro/raw/master/dist/phigaro-%s.tar.gz" % version ) -with open(tag_file, 'w') as f: - f.write('v%s' % version) +with open(tag_file, "w") as f: + f.write("v%s" % version) diff --git a/tag_name b/tag_name index a6316f0..fa49670 100644 --- a/tag_name +++ b/tag_name @@ -1 +1 @@ -v2.3.0 \ No newline at end of file +v2.4.0 \ No newline at end of file diff --git a/test_data_gitaction/latest_version.txt b/test_data_gitaction/latest_version.txt index 7f974b1..ce39b86 100644 --- a/test_data_gitaction/latest_version.txt +++ b/test_data_gitaction/latest_version.txt @@ -1 +1 @@ -https://github.com/bobeobibo/phigaro/raw/master/dist/phigaro-2.3.0.tar.gz \ No newline at end of file +https://github.com/bobeobibo/phigaro/raw/master/dist/phigaro-2.4.0.tar.gz \ No newline at end of file diff --git a/tox.ini b/tox.ini new file mode 100644 index 0000000..6bf9dbc --- /dev/null +++ b/tox.ini @@ -0,0 +1,17 @@ +[tox] +min_version = 4 +envlist = + format + py27, py3.5.0, py3.5.10, py3.6.0, py3.6.15, py3.7.0, py3.7.17, py3.8.0, py3.8.18, py3.9.0, py3.9.18, py3.10.0, py3.10.13, py3.11.0, py3.11.7, py3.12.0, py3.12.1 +skipsdist = false + +[testenv] +commands = + phigaro --help + +[testenv:format] +description = install black in a virtual environment and invoke it on the current folder +deps = black==22.3.0 +skip_install = true +commands = black . + diff --git a/version_tracker.md b/version_tracker.md index b2e4ec2..233659a 100644 --- a/version_tracker.md +++ b/version_tracker.md @@ -1,3 +1,12 @@ +## V2.4.0 +- Restored a compatibility with Python versions `> 3.7.1`. +- `.pickle` files, containing data neccasary for the work of the tool, were replaced with `.json` and `.csv` files to resolve compatibility issues. +- Added prophage IDs across outputs to improve compatibility between files. +- Fixed a bug with `gff3` and `bed` files formats: prophage coordinates were shifted by 1 nucleotide upstream in versions `phigaro <= 2.3.0`. + +## V2.3.0 +Added a `--save-fasta` option. + ## V2.2.6 Minor corrections. Docker & Singularity containers. What_the_phage implementation.
{7} {1} - {2}
@@ -534,9 +534,9 @@