diff --git a/.pydevproject b/.pydevproject
index c3434da..ad74947 100644
--- a/.pydevproject
+++ b/.pydevproject
@@ -3,6 +3,6 @@
/${PROJECT_DIR_NAME}
-python 3.0
+python interpreter
Default
diff --git a/pyreference/reference.py b/pyreference/reference.py
index 9b828a3..fc538e3 100644
--- a/pyreference/reference.py
+++ b/pyreference/reference.py
@@ -1,7 +1,8 @@
from __future__ import print_function, absolute_import
import HTSeq
-from deprecated import deprecated
+from functools import reduce
+from deprecation import deprecated
import gzip
import json
from lazy import lazy
@@ -88,7 +89,7 @@ def __init__(self, build=None, config=None, **kwargs):
params = load_params_from_config(build=build, config=config)
except OSError as e:
config_exception = e
- params = {}
+ params = {"build" : build}
# Set / Overwrite with non-null kwargs
params.update({k : v for (k,v) in kwargs.items() if v is not None})
@@ -191,11 +192,11 @@ def get_gene_by_name(self, gene_name):
return self.get_gene_by_id(gene_id)
- #@deprecated(reason="Use get_gene_by_id")
+ #@deprecated(details="Use get_gene_by_id")
def get_gene(self, gene_id):
return self.get_gene_by_id(gene_id)
- #@deprecated(reason="Use get_transcript_by_id")
+ #@deprecated(details="Use get_transcript_by_id")
def get_transcript(self, transcript_id):
return self.get_transcript_by_id(transcript_id)
@@ -349,7 +350,7 @@ def get_best_region(self, iv):
break
return region
- @deprecated(reason="Use get_best_region()")
+ @deprecated(details="Use get_best_region()")
def get_region(self, iv):
return self.get_best_region(iv)
diff --git a/pyreference/tests/reference/hg19_chrY_300kb_genes.gtf.json.gz b/pyreference/tests/reference/hg19_chrY_300kb_genes.gtf.json.gz
index 51a8487..08ae36c 100644
Binary files a/pyreference/tests/reference/hg19_chrY_300kb_genes.gtf.json.gz and b/pyreference/tests/reference/hg19_chrY_300kb_genes.gtf.json.gz differ
diff --git a/pyreference/tests/test_reference.py b/pyreference/tests/test_reference.py
index 9cee748..75561e8 100644
--- a/pyreference/tests/test_reference.py
+++ b/pyreference/tests/test_reference.py
@@ -65,7 +65,7 @@ def test_genes(self):
"3p_utr" : "CGCCGCCCGC" },
}
- for test in test_cases.itervalues():
+ for test in six.itervalues(test_cases):
transcript = self.reference.transcripts[test["transcript_id"]]
utr = str(transcript.get_3putr_sequence()).upper()
diff --git a/pyreference/transcript.py b/pyreference/transcript.py
index 612f2e9..49e5605 100644
--- a/pyreference/transcript.py
+++ b/pyreference/transcript.py
@@ -1,7 +1,7 @@
from __future__ import print_function, absolute_import
import HTSeq
-#from deprecated import deprecated
+#from from deprecation import deprecated
from lazy import lazy
from pyreference.genomic_region import GenomicRegion
@@ -37,7 +37,7 @@ def get_features_length(self, feature_type):
length += feature[END] - feature[START]
return length
- #@deprecated(reason="Use get_features_in_stranded_order")
+ #@deprecated(details="Use get_features_in_stranded_order")
def get_features(self, feature_type):
''' returns list of HTSeq.GenomicFeature '''
genomic_features = []
@@ -76,7 +76,7 @@ def get_features_in_stranded_order(self, feature_type):
def length(self):
return self.get_features_length("exon")
- #@deprecated(reason="Use Transcript.length")
+ #@deprecated(details="Use Transcript.length")
def get_transcript_length(self):
return self.length
diff --git a/pyreference/utils/file_utils.py b/pyreference/utils/file_utils.py
index 99bbedd..6418437 100644
--- a/pyreference/utils/file_utils.py
+++ b/pyreference/utils/file_utils.py
@@ -3,14 +3,15 @@
@author: dlawrence
'''
-from md5 import md5
+from hashlib import md5
import os
+import six
try:
- from pathlib import Path
+ from pathlib import Path #@UnresolvedImport
except (ImportError,AttributeError):
- from pathlib2 import Path
+ from pathlib2 import Path #@UnresolvedImport
def name_from_file_name(file_name):
return Path(file_name).name
@@ -26,12 +27,12 @@ def mk_path_for_file(f):
mk_path(os.path.dirname(f))
def file_or_file_name(f, mode='r'):
- if isinstance(f, basestring): # Works on unicode
+ if isinstance(f, six.string_types):
if 'w' in mode: # Create path if writing
mk_path_for_file(f)
return open(f, mode)
- elif isinstance(f, file):
+ elif hasattr(f, 'read'):
return f # Already a File object
else:
raise ValueError("'%s' (%s) not a file or string" % (f, type(f)))
diff --git a/pyreference/utils/genomics_utils.py b/pyreference/utils/genomics_utils.py
index a193d79..2d133dd 100644
--- a/pyreference/utils/genomics_utils.py
+++ b/pyreference/utils/genomics_utils.py
@@ -6,6 +6,11 @@
from Bio import SeqIO
import HTSeq
+try:
+ from sys import intern
+except (ImportError,AttributeError):
+ pass
+
from pyreference.settings import CHROM, START, END, STRAND
diff --git a/requirements.txt b/requirements.txt
index 87ef713..6791cf8 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,6 @@
biopython
configargparse
-deprecated
+deprecation
HTSeq
lazy
pyfasta
diff --git a/setup.py b/setup.py
index 3fb350c..1a09633 100644
--- a/setup.py
+++ b/setup.py
@@ -4,7 +4,7 @@
setup(name = 'pyreference',
packages = find_packages(),
- version = '0.3',
+ version = '0.4',
description = 'Library for working with reference genomes',
author = 'David Lawrence',
author_email = 'davmlaw@gmail.com',
@@ -14,7 +14,7 @@
install_requires=[
'biopython',
'configargparse',
- 'deprecated',
+ 'deprecation',
'HTSeq',
'lazy',
'pyfasta',