[med-svn] [Git][med-team/python-bcbio-gff][master] 5 commits: routine-update: New upstream version
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Feb 17 19:04:34 GMT 2024
Étienne Mollier pushed to branch master at Debian Med / python-bcbio-gff
Commits:
41284fa6 by Étienne Mollier at 2024-02-17T19:37:53+01:00
routine-update: New upstream version
- - - - -
5d2ad5c2 by Étienne Mollier at 2024-02-17T19:37:54+01:00
New upstream version 0.7.1
- - - - -
5710b05c by Étienne Mollier at 2024-02-17T19:37:54+01:00
Update upstream source from tag 'upstream/0.7.1'
Update to upstream version '0.7.1'
with Debian dir 417d48722e36b983fb91f144e201c4548f9bdfaf
- - - - -
88c367c9 by Étienne Mollier at 2024-02-17T19:37:57+01:00
routine-update: Build-Depends: s/dh-python/dh-sequence-python3/
- - - - -
732c730d by Étienne Mollier at 2024-02-17T19:40:36+01:00
routine-update: Ready to upload to unstable
- - - - -
8 changed files:
- BCBio/GFF/GFFOutput.py
- BCBio/GFF/GFFParser.py
- BCBio/GFF/__init__.py
- PKG-INFO
- bcbio_gff.egg-info/PKG-INFO
- debian/changelog
- debian/control
- debian/rules
Changes:
=====================================
BCBio/GFF/GFFOutput.py
=====================================
@@ -121,9 +121,9 @@ class GFF3Writer:
parent_id=None):
"""Write a feature with location information.
"""
- if feature.strand == 1:
+ if feature.location.strand == 1:
strand = '+'
- elif feature.strand == -1:
+ elif feature.location.strand == -1:
strand = '-'
else:
strand = '.'
@@ -145,8 +145,8 @@ class GFF3Writer:
parts = [str(rec_id),
feature.qualifiers.get("source", ["feature"])[0],
ftype,
- str(feature.location.nofuzzy_start + 1), # 1-based indexing
- str(feature.location.nofuzzy_end),
+ str(feature.location.start + 1), # 1-based indexing
+ str(feature.location.end),
feature.qualifiers.get("score", ["."])[0],
strand,
self._get_phase(feature),
=====================================
BCBio/GFF/GFFParser.py
=====================================
@@ -21,7 +21,6 @@ import re
import collections
import io
import itertools
-import warnings
import six
from six.moves import urllib
# Make defaultdict compatible with versions of python older than 2.4
@@ -43,8 +42,6 @@ except ImportError:
from Bio.SeqRecord import SeqRecord
from Bio import SeqFeature
from Bio import SeqIO
-from Bio import BiopythonDeprecationWarning
-warnings.simplefilter("ignore", BiopythonDeprecationWarning)
def _gff_line_map(line, params):
"""Map part of Map-Reduce; parses a line of GFF into a dictionary.
@@ -468,7 +465,7 @@ class _AbstractMapReduceGFF:
# one child, do not nest it
if len(cur_children) == 1:
rec_id, child = cur_children[0]
- loc = (child.location.nofuzzy_start, child.location.nofuzzy_end)
+ loc = (child.location.start, child.location.end)
rec, base = self._get_rec(base,
dict(rec_id=rec_id, location=loc))
rec.features.append(child)
@@ -564,13 +561,13 @@ class _AbstractMapReduceGFF:
"""Add a new feature that is missing from the GFF file.
"""
base_rec_id = list(set(c[0] for c in cur_children))
- child_strands = list(set(c[1].strand for c in cur_children))
+ child_strands = list(set(c[1].location.strand for c in cur_children))
inferred_strand = child_strands[0] if len(child_strands) == 1 else None
assert len(base_rec_id) > 0
feature_dict = dict(id=parent_id, strand=inferred_strand,
type="inferred_parent", quals=dict(ID=[parent_id]),
rec_id=base_rec_id[0])
- coords = [(c.location.nofuzzy_start, c.location.nofuzzy_end)
+ coords = [(c.location.start, c.location.end)
for r, c in cur_children]
feature_dict["location"] = (min([c[0] for c in coords]),
max([c[1] for c in coords]))
@@ -587,9 +584,10 @@ class _AbstractMapReduceGFF:
def _get_feature(self, feature_dict):
"""Retrieve a Biopython feature from our dictionary representation.
"""
- location = SeqFeature.FeatureLocation(*feature_dict['location'])
- new_feature = SeqFeature.SeqFeature(location, feature_dict['type'],
- id=feature_dict['id'], strand=feature_dict['strand'])
+ #location = SeqFeature.FeatureLocation(*feature_dict['location'])
+ rstart, rend = feature_dict['location']
+ new_feature = SeqFeature.SeqFeature(SeqFeature.SimpleLocation(start=rstart, end=rend, strand=feature_dict['strand']), feature_dict['type'],
+ id=feature_dict['id'])
# Support for Biopython 1.68 and above, which removed sub_features
if not hasattr(new_feature, "sub_features"):
new_feature.sub_features = []
=====================================
BCBio/GFF/__init__.py
=====================================
@@ -3,4 +3,4 @@
from BCBio.GFF.GFFParser import GFFParser, DiscoGFFParser, GFFExaminer, parse, parse_simple
from BCBio.GFF.GFFOutput import GFF3Writer, write
-__version__ = "0.7.0"
+__version__ = "0.7.1"
=====================================
PKG-INFO
=====================================
@@ -1,9 +1,11 @@
Metadata-Version: 2.1
Name: bcbio-gff
-Version: 0.7.0
+Version: 0.7.1
Summary: Read and write Generic Feature Format (GFF) with Biopython integration.
Home-page: https://github.com/chapmanb/bcbb/tree/master/gff
Author: Brad Chapman
Author-email: chapmanb at 50mail.com
License: Biopython License
License-File: LICENSE
+Requires-Dist: six
+Requires-Dist: biopython
=====================================
bcbio_gff.egg-info/PKG-INFO
=====================================
@@ -1,9 +1,11 @@
Metadata-Version: 2.1
Name: bcbio-gff
-Version: 0.7.0
+Version: 0.7.1
Summary: Read and write Generic Feature Format (GFF) with Biopython integration.
Home-page: https://github.com/chapmanb/bcbb/tree/master/gff
Author: Brad Chapman
Author-email: chapmanb at 50mail.com
License: Biopython License
License-File: LICENSE
+Requires-Dist: six
+Requires-Dist: biopython
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-bcbio-gff (0.7.1-1) unstable; urgency=medium
+
+ * New upstream version
+ * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 17 Feb 2024 19:38:03 +0100
+
python-bcbio-gff (0.7.0-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Section: science
Testsuite: autopkgtest-pkg-python
Priority: optional
Build-Depends: debhelper-compat (= 13),
- dh-python,
+ dh-sequence-python3,
python3-all,
python3-setuptools,
python3-biopython,
=====================================
debian/rules
=====================================
@@ -5,7 +5,7 @@
export PYBUILD_NAME=bcbio-gff
%:
- dh $@ --with python3 --buildsystem=pybuild
+ dh $@ --buildsystem=pybuild
override_dh_install:
dh_install
View it on GitLab: https://salsa.debian.org/med-team/python-bcbio-gff/-/compare/ec5fbdcaa00e1e8105e9ecdce22f0e18390ca3fd...732c730d1f859c2b7ad2453d79c8cd4f14aa4b3d
--
View it on GitLab: https://salsa.debian.org/med-team/python-bcbio-gff/-/compare/ec5fbdcaa00e1e8105e9ecdce22f0e18390ca3fd...732c730d1f859c2b7ad2453d79c8cd4f14aa4b3d
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