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117 changes: 117 additions & 0 deletions
117
src/python/ensembl/genes/metadata/check_for_transcriptomic_batch.py
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| # See the NOTICE file distributed with this work for additional information #pylint: disable=missing-module-docstring | ||
| # regarding copyright ownership. | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 (the "License"); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
| """Check the availability for short and long read data from ENA website given a taxon id""" | ||
| import os.path | ||
| from pathlib import Path | ||
| from typing import List | ||
| import argparse | ||
| import requests | ||
|
|
||
| def ena_rest_api(query:str, taxon_id: int, batching_option:bool, batch_size:int , output_dir_path:Path)->int: | ||
| search_url = f"https://www.ebi.ac.uk/ena/portal/api/search?display=report&query={query}&domain=read&result=read_run&fields=run_accession" # pylint: disable=line-too-long | ||
| #def searchUrl = "https://www.ebi.ac.uk/ena/portal/api/search?result=read_run&query=${taxonQuery}%20AND%20instrument_platform=ILLUMINA%20AND%20library_layout=PAIRED%20AND%20library_source=TRANSCRIPTOMIC%20AND%20 | ||
| #first_created%3E=${lastCheckedDate.trim()}&domain=read&fields=run_accession" | ||
|
|
||
| search_result = requests.get(search_url) | ||
| results = search_result.text.strip().split("\n")[1:] | ||
| # If batching is enabled, split the results based on batch_size | ||
| if batching_option and batch_size > 0: | ||
| batches = [results[i:i + batch_size] for i in range(0, len(results), batch_size)] | ||
| output_dir = output_dir_path / taxon_id / "batch" | ||
| # Create the directory structure if it doesn't exist | ||
| output_dir.mkdir(parents=True, exist_ok=True) | ||
| # Save each batch into a separate file | ||
| for idx, batch in enumerate(batches): | ||
| batch_file = output_dir / f"batch_{idx + 1}.txt" | ||
| with open(batch_file, 'w') as f: | ||
| f.write("\n".join(batch)) | ||
| return len(results) | ||
|
|
||
| def check_data_from_ena(# pylint: disable=too-many-locals | ||
| taxon_id: int, | ||
| tree: bool, | ||
| batching_option:bool, batch_size:int, output_dir:Path | ||
| ) -> None: | ||
| """Query ENA API to get short or long read data""" | ||
|
|
||
| if tree: | ||
| query = f"tax_tree({taxon_id})" | ||
| else: | ||
| query = f"tax_eq({taxon_id})" | ||
|
|
||
| query_short_paired=query+f" AND instrument_platform=ILLUMINA AND library_layout=PAIRED AND library_source=TRANSCRIPTOMIC AND first_created>=2019-01-01" | ||
| query_short_single=query+f" AND instrument_platform=ILLUMINA AND library_layout=SINGLE AND library_source=TRANSCRIPTOMIC AND first_created>=2019-01-01" | ||
| query_pacbio=query+f" AND instrument_platform=PACBIO_SMRT AND library_source=TRANSCRIPTOMIC AND first_created>=2019-01-01" | ||
| query_onp=query+f" AND instrument_platform=OXFORD_NANOPORE AND library_source=TRANSCRIPTOMIC AND first_created>=2019-01-01" | ||
|
|
||
| short_paired_runs=ena_rest_api(query_short_paired, taxon_id, batching_option, batch_size, output_dir) | ||
| short_single_runs=ena_rest_api(query_short_single, taxon_id, batching_option, batch_size, output_dir) | ||
| pacbio_read_runs =ena_rest_api(query_pacbio, taxon_id, batching_option, batch_size, output_dir) | ||
| onp_read_runs=ena_rest_api(query_onp, taxon_id, batching_option, batch_size, output_dir) | ||
|
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||
| print(f"{taxon_id};Short-read paired-end illumina;{short_paired_runs};Short-read single-end illumina;{short_single_runs};Long-read PacBio;{pacbio_read_runs};Long_read ONP;{onp_read_runs}") | ||
| #print (text.BOLD+f"Short-read paired-end illumina data available! "+text.END+f"Found {short_paired_runs} runs.") | ||
| #print (text.BOLD+f"Short-read single-end illumina data available! "+text.END+f"Found {short_single_runs} runs.") | ||
| #print (text.BOLD+f"Long-read PacBio data available! "+text.END+f"Found {pacbio_read_runs} runs.") | ||
| #print (text.BOLD+f"Long_read ONP data available! "+text.END+f"Found {onp_read_runs} runs.") | ||
|
|
||
| class text: | ||
| """formatting set""" | ||
|
|
||
| BOLD = "\033[1m" | ||
| UNDERLINE = "\033[4m" | ||
| END = "\033[0m" | ||
|
|
||
|
|
||
| class InputSchema(argparse.ArgumentParser): | ||
| """Input arguments""" | ||
| def __init__(self): | ||
| super().__init__() | ||
|
|
||
| self.add_argument( | ||
| "-t", "--taxon_id", type=str, required=False, help="Taxon id" | ||
| ) | ||
|
|
||
| self.add_argument( | ||
| "--tree", action='store_true', required=False, help="Turn on the 'Include subordinate taxa' option in your query to ENA" | ||
| ) | ||
| self.add_argument( | ||
| "--output_dir", required=False, help="Output directory path" | ||
| ) | ||
| self.add_argument( | ||
| "--batching_option", type=bool, required=False, help="Batch run accession" | ||
| ) | ||
| self.add_argument( | ||
| "--batch_size", type=int, required=False, help="Batch size" | ||
| ) | ||
| self.add_argument( | ||
| "-f", "--file", type=str, required=False, help="Path to the file containing a list of taxon ids" | ||
| ) | ||
|
|
||
| def main() -> None: | ||
| """Entrypoint""" | ||
| parser=InputSchema() | ||
| args = parser.parse_args() | ||
| if args.file: | ||
| with open(args.file, 'r') as input_file: | ||
| taxon_ids=input_file.read().splitlines() | ||
| for taxon_id in taxon_ids: | ||
| check_data_from_ena(taxon_id, args.tree, args.batching_option, args.batch_size, Path(args.output_dir)) | ||
| else: | ||
| check_data_from_ena(args.taxon_id, args.tree, args.batching_option, args.batch_size, Path(args.output_dir)) | ||
|
|
||
| if __name__ == "__main__": | ||
| main() | ||
|
|