[med-svn] [Git][med-team/python-gtfparse][master] 7 commits: routine-update: New upstream version
Mohd Bilal (@rmb)
gitlab at salsa.debian.org
Sun Dec 4 13:00:55 GMT 2022
Mohd Bilal pushed to branch master at Debian Med / python-gtfparse
Commits:
ca87d34f by Mohammed Bilal at 2022-12-04T10:54:29+00:00
routine-update: New upstream version
- - - - -
b47cfcb2 by Mohammed Bilal at 2022-12-04T11:39:27+00:00
New upstream version 1.3.0+ds
- - - - -
ed3c0318 by Mohammed Bilal at 2022-12-04T11:39:33+00:00
routine-update: Standards-Version: 4.6.1
- - - - -
bb8883da by Mohammed Bilal at 2022-12-04T11:39:33+00:00
d/{,t/}control: depend on pytest instead of nose
Closes: #1018506
- - - - -
6d620369 by Mohammed Bilal at 2022-12-04T12:18:32+00:00
add patch to support pytest
- - - - -
0dc53838 by Mohammed Bilal at 2022-12-04T18:21:47+05:30
run autopkgtest,build-time tests with pytest
- - - - -
2401aa1f by Mohammed Bilal at 2022-12-04T18:21:53+05:30
prepare changelog for 1.3.0+ds-1
- - - - -
19 changed files:
- + LICENSE
- PKG-INFO
- README.md
- debian/changelog
- debian/control
- + debian/patches/series
- + debian/patches/switch-to-pytest.patch
- debian/rules
- debian/tests/control
- debian/tests/run-unit-test
- gtfparse.egg-info/PKG-INFO
- gtfparse/__init__.py
- gtfparse/attribute_parsing.py
- gtfparse/create_missing_features.py
- gtfparse/parsing_error.py
- gtfparse/read_gtf.py
- gtfparse/required_columns.py
- + gtfparse/version.py
- setup.py
Changes:
=====================================
LICENSE
=====================================
@@ -0,0 +1,202 @@
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=====================================
PKG-INFO
=====================================
@@ -1,56 +1,10 @@
Metadata-Version: 2.1
Name: gtfparse
-Version: 1.2.1
+Version: 1.3.0
Summary: GTF Parsing
Home-page: https://github.com/openvax/gtfparse
Author: Alex Rubinsteyn
License: http://www.apache.org/licenses/LICENSE-2.0.html
-Description: [](https://travis-ci.org/openvax/gtfparse) [](https://coveralls.io/github/openvax/gtfparse?branch=master)
- <a href="https://pypi.python.org/pypi/gtfparse/">
- <img src="https://img.shields.io/pypi/v/gtfparse.svg?maxAge=1000" alt="PyPI" />
- </a>
-
- gtfparse
- ========
- Parsing tools for GTF (gene transfer format) files.
-
- # Example usage
-
- ## Parsing all rows of a GTF file into a Pandas DataFrame
-
- ```python
- from gtfparse import read_gtf
-
- # returns GTF with essential columns such as "feature", "seqname", "start", "end"
- # alongside the names of any optional keys which appeared in the attribute column
- df = read_gtf("gene_annotations.gtf")
-
- # filter DataFrame to gene entries on chrY
- df_genes = df[df["feature"] == "gene"]
- df_genes_chrY = df_genes[df_genes["seqname"] == "Y"]
- ```
-
-
- ## Getting gene FPKM values from a StringTie GTF file
-
- ```python
- from gtfparse import read_gtf
-
- df = read_gtf(
- "stringtie-output.gtf",
- column_converters={"FPKM": float})
-
- gene_fpkms = {
- gene_name: fpkm
- for (gene_name, fpkm, feature)
- in zip(df["gene_name"], df["FPKM"], df["feature"])
- if feature == "gene"
- }
- ```
-
-
-
-Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
@@ -59,3 +13,49 @@ Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
+License-File: LICENSE
+
+[](https://travis-ci.org/openvax/gtfparse) [](https://coveralls.io/github/openvax/gtfparse?branch=master)
+<a href="https://pypi.python.org/pypi/gtfparse/">
+ <img src="https://img.shields.io/pypi/v/gtfparse.svg?maxAge=1000" alt="PyPI" />
+</a>
+
+gtfparse
+========
+Parsing tools for GTF (gene transfer format) files.
+
+# Example usage
+
+## Parsing all rows of a GTF file into a Pandas DataFrame
+
+```python
+from gtfparse import read_gtf
+
+# returns GTF with essential columns such as "feature", "seqname", "start", "end"
+# alongside the names of any optional keys which appeared in the attribute column
+df = read_gtf("gene_annotations.gtf")
+
+# filter DataFrame to gene entries on chrY
+df_genes = df[df["feature"] == "gene"]
+df_genes_chrY = df_genes[df_genes["seqname"] == "Y"]
+```
+
+
+## Getting gene FPKM values from a StringTie GTF file
+
+```python
+from gtfparse import read_gtf
+
+df = read_gtf(
+ "Transcripts.gtf",
+ column_converters={"FPKM": float})
+
+gene_fpkms = {
+ gene_name: fpkm
+ for (gene_name, fpkm, feature)
+ in zip(df["seqname"], df["FPKM"], df["feature"])
+ if feature == "gene"
+}
+```
+
+
=====================================
README.md
=====================================
@@ -30,13 +30,13 @@ df_genes_chrY = df_genes[df_genes["seqname"] == "Y"]
from gtfparse import read_gtf
df = read_gtf(
- "stringtie-output.gtf",
+ "Transcripts.gtf",
column_converters={"FPKM": float})
gene_fpkms = {
gene_name: fpkm
for (gene_name, fpkm, feature)
- in zip(df["gene_name"], df["FPKM"], df["feature"])
+ in zip(df["seqname"], df["FPKM"], df["feature"])
if feature == "gene"
}
```
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+python-gtfparse (1.3.0+ds-1) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * New upstream version 1.3.0+ds
+ * d/control: Standards-Version: 4.6.1 (routine-update)
+ * d/{,t/}control: depend on pytest instead of nose (Closes: #1018506)
+ * d/patches/: add patch to support pytest
+ * d/{rules,t/run-unit-test}: run autopkgtest,build-time tests with pytest
+
+ -- Mohammed Bilal <mdbilal at disroot.org> Sun, 04 Dec 2022 11:01:41 +0000
+
python-gtfparse (1.2.1+ds-2) unstable; urgency=medium
* Team Upload.
=====================================
debian/control
=====================================
@@ -3,8 +3,8 @@ Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper-compat (= 13), dh-python, python3-setuptools, python3-all, python3-six, python3-pandas, python3-nose
-Standards-Version: 4.5.1
+Build-Depends: debhelper-compat (= 13), dh-python, python3-setuptools, python3-all, python3-six, python3-pandas, python3-pytest
+Standards-Version: 4.6.1
Homepage: https://github.com/openvax/gtfparse
Vcs-Browser: https://salsa.debian.org/med-team/python-gtfparse
Vcs-Git: https://salsa.debian.org/med-team/python-gtfparse.git
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+switch-to-pytest.patch
=====================================
debian/patches/switch-to-pytest.patch
=====================================
@@ -0,0 +1,141 @@
+Description: Switch to pytest from nose since the latter is now deprecated
+Author: Mohammed Bilal <mdbilal at disroot.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1018506
+Forwarded: https://github.com/openvax/gtfparse/issues/29
+Last-Update: 2022-12-04
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/test/test_expand_attributes.py
++++ b/test/test_expand_attributes.py
+@@ -1,5 +1,4 @@
+ from gtfparse import expand_attribute_strings
+-from nose.tools import eq_
+
+ def test_attributes_in_quotes():
+ attributes = [
+@@ -7,10 +6,10 @@
+ "gene_id \"ENSG002\"; tag \"wolfpuppy\"; version \"2\";"
+ ]
+ parsed_dict = expand_attribute_strings(attributes)
+- eq_(list(sorted(parsed_dict.keys())), ["gene_id", "tag", "version"])
+- eq_(parsed_dict["gene_id"], ["ENSG001", "ENSG002"])
+- eq_(parsed_dict["tag"], ["bogotron", "wolfpuppy"])
+- eq_(parsed_dict["version"], ["1", "2"])
++ assert list(sorted(parsed_dict.keys())), ["gene_id", "tag", "version"]
++ assert parsed_dict["gene_id"], ["ENSG001", "ENSG002"]
++ assert parsed_dict["tag"], ["bogotron", "wolfpuppy"]
++ assert parsed_dict["version"], ["1", "2"]
+
+
+ def test_attributes_without_quotes():
+@@ -19,10 +18,10 @@
+ "gene_id ENSG002; tag wolfpuppy; version 2"
+ ]
+ parsed_dict = expand_attribute_strings(attributes)
+- eq_(list(sorted(parsed_dict.keys())), ["gene_id", "tag", "version"])
+- eq_(parsed_dict["gene_id"], ["ENSG001", "ENSG002"])
+- eq_(parsed_dict["tag"], ["bogotron", "wolfpuppy"])
+- eq_(parsed_dict["version"], ["1", "2"])
++ assert list(sorted(parsed_dict.keys())), ["gene_id", "tag", "version"]
++ assert parsed_dict["gene_id"], ["ENSG001", "ENSG002"]
++ assert parsed_dict["tag"], ["bogotron", "wolfpuppy"]
++ assert parsed_dict["version"], ["1", "2"]
+
+
+ def test_optional_attributes():
+@@ -32,6 +31,6 @@
+ "gene_id ENSG003; sometimes-present wolfpuppy;",
+ ]
+ parsed_dict = expand_attribute_strings(attributes)
+- eq_(list(sorted(parsed_dict.keys())), ["gene_id", "sometimes-present"])
+- eq_(parsed_dict["gene_id"], ["ENSG001", "ENSG002", "ENSG003"])
+- eq_(parsed_dict["sometimes-present"], ["bogotron", "", "wolfpuppy"])
++ assert list(sorted(parsed_dict.keys())), ["gene_id", "sometimes-present"]
++ assert parsed_dict["gene_id"], ["ENSG001", "ENSG002", "ENSG003"]
++ assert parsed_dict["sometimes-present"], ["bogotron", "", "wolfpuppy"]
+--- a/test/test_multiple_values_for_tag_attribute.py
++++ b/test/test_multiple_values_for_tag_attribute.py
+@@ -1,6 +1,5 @@
+ from six import StringIO
+ from gtfparse import parse_gtf_and_expand_attributes
+-from nose.tools import eq_
+
+ # failing example from https://github.com/openvax/gtfparse/issues/2
+ GTF_TEXT = (
+@@ -15,18 +14,18 @@
+ def test_parse_tag_attributes():
+ parsed = parse_gtf_and_expand_attributes(StringIO(GTF_TEXT))
+ tag_column = parsed["tag"]
+- eq_(len(tag_column), 1)
++ assert len(tag_column), 1
+ tags = tag_column[0]
+- eq_(tags, 'cds_end_NF,mRNA_end_NF')
++ assert tags, 'cds_end_NF,mRNA_end_NF'
+
+ def test_parse_tag_attributes_with_usecols():
+ parsed = parse_gtf_and_expand_attributes(
+ StringIO(GTF_TEXT),
+ restrict_attribute_columns=["tag"])
+ tag_column = parsed["tag"]
+- eq_(len(tag_column), 1)
++ assert len(tag_column), 1
+ tags = tag_column[0]
+- eq_(tags, 'cds_end_NF,mRNA_end_NF')
++ assert tags, 'cds_end_NF,mRNA_end_NF'
+
+ def test_parse_tag_attributes_with_usecols_other_column():
+ parsed = parse_gtf_and_expand_attributes(
+--- a/test/test_parse_gtf_lines.py
++++ b/test/test_parse_gtf_lines.py
+@@ -1,5 +1,4 @@
+ import numpy as np
+-from nose.tools import eq_, assert_raises
+ from gtfparse import (
+ parse_gtf,
+ parse_gtf_and_expand_attributes,
+@@ -7,6 +6,7 @@
+ ParsingError
+ )
+ from six import StringIO
++from pytest import raises as assert_raises
+
+ gtf_text = """
+ # sample GTF data copied from:
+@@ -28,27 +28,27 @@
+ "transcript_source",
+ ]
+ # convert to list since Py3's dictionary keys are a distinct collection type
+- eq_(list(parsed_dict.keys()), expected_columns)
+- eq_(list(parsed_dict["seqname"]), ["1", "1"])
++ assert list(parsed_dict.keys()), expected_columns
++ assert list(parsed_dict["seqname"]), ["1", "1"]
+ # convert to list for comparison since numerical columns may be NumPy arrays
+- eq_(list(parsed_dict["start"]), [11869, 11869])
+- eq_(list(parsed_dict["end"]), [14409, 14409])
++ assert list(parsed_dict["start"]), [11869, 11869]
++ assert list(parsed_dict["end"]), [14409, 14409]
+ # can't compare NaN with equality
+ scores = list(parsed_dict["score"])
+ assert np.isnan(scores).all(), "Unexpected scores: %s" % scores
+- eq_(list(parsed_dict["gene_id"]), ["ENSG00000223972", "ENSG00000223972"])
+- eq_(list(parsed_dict["transcript_id"]), ["", "ENST00000456328"])
++ assert list(parsed_dict["gene_id"]), ["ENSG00000223972", "ENSG00000223972"]
++ assert list(parsed_dict["transcript_id"]), ["", "ENST00000456328"]
+
+
+ def test_parse_gtf_lines_without_expand_attributes():
+ parsed_dict = parse_gtf(StringIO(gtf_text))
+
+ # convert to list since Py3's dictionary keys are a distinct collection type
+- eq_(list(parsed_dict.keys()), REQUIRED_COLUMNS)
+- eq_(list(parsed_dict["seqname"]), ["1", "1"])
++ assert list(parsed_dict.keys()), REQUIRED_COLUMNS
++ assert list(parsed_dict["seqname"]), ["1", "1"]
+ # convert to list for comparison since numerical columns may be NumPy arrays
+- eq_(list(parsed_dict["start"]), [11869, 11869])
+- eq_(list(parsed_dict["end"]), [14409, 14409])
++ assert list(parsed_dict["start"]), [11869, 11869]
++ assert list(parsed_dict["end"]), [14409, 14409]
+ # can't compare NaN with equality
+ scores = list(parsed_dict["score"])
+ assert np.isnan(scores).all(), "Unexpected scores: %s" % scores
=====================================
debian/rules
=====================================
@@ -9,7 +9,7 @@ override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
# This is done because data/ dir is not vendored on pypi
rm -f test/test_refseq_gtf.py test/test_ensembl_gtf.py test/test_read_stringtie_gtf.py
- nosetests3
+ PYTHONPATH=$(CURDIR) pytest-3 -v
endif
override_dh_auto_clean:
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, python3-nose
+Depends: @, python3-pytest
Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -2,10 +2,10 @@
set -e
for py in $(py3versions -r 2> /dev/null)
do echo "Testing with $py in $(pwd):"
-nosetests3 -v test/test_create_missing_features.py
-nosetests3 -v test/test_expand_attributes.py
-nosetests3 -v test/test_multiple_values_for_tag_attribute.py
-nosetests3 -v test/test_parse_gtf_lines.py
+pytest-3 -v test/test_create_missing_features.py
+pytest-3 -v test/test_expand_attributes.py
+pytest-3 -v test/test_multiple_values_for_tag_attribute.py
+pytest-3 -v test/test_parse_gtf_lines.py
done
-#This is done because data/ dir is not vendored on pypi as mentioned in d/rules
\ No newline at end of file
+#This is done because data/ dir is not vendored on pypi as mentioned in d/rules
=====================================
gtfparse.egg-info/PKG-INFO
=====================================
@@ -1,56 +1,10 @@
Metadata-Version: 2.1
Name: gtfparse
-Version: 1.2.1
+Version: 1.3.0
Summary: GTF Parsing
Home-page: https://github.com/openvax/gtfparse
Author: Alex Rubinsteyn
License: http://www.apache.org/licenses/LICENSE-2.0.html
-Description: [](https://travis-ci.org/openvax/gtfparse) [](https://coveralls.io/github/openvax/gtfparse?branch=master)
- <a href="https://pypi.python.org/pypi/gtfparse/">
- <img src="https://img.shields.io/pypi/v/gtfparse.svg?maxAge=1000" alt="PyPI" />
- </a>
-
- gtfparse
- ========
- Parsing tools for GTF (gene transfer format) files.
-
- # Example usage
-
- ## Parsing all rows of a GTF file into a Pandas DataFrame
-
- ```python
- from gtfparse import read_gtf
-
- # returns GTF with essential columns such as "feature", "seqname", "start", "end"
- # alongside the names of any optional keys which appeared in the attribute column
- df = read_gtf("gene_annotations.gtf")
-
- # filter DataFrame to gene entries on chrY
- df_genes = df[df["feature"] == "gene"]
- df_genes_chrY = df_genes[df_genes["seqname"] == "Y"]
- ```
-
-
- ## Getting gene FPKM values from a StringTie GTF file
-
- ```python
- from gtfparse import read_gtf
-
- df = read_gtf(
- "stringtie-output.gtf",
- column_converters={"FPKM": float})
-
- gene_fpkms = {
- gene_name: fpkm
- for (gene_name, fpkm, feature)
- in zip(df["gene_name"], df["FPKM"], df["feature"])
- if feature == "gene"
- }
- ```
-
-
-
-Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
@@ -59,3 +13,49 @@ Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
+License-File: LICENSE
+
+[](https://travis-ci.org/openvax/gtfparse) [](https://coveralls.io/github/openvax/gtfparse?branch=master)
+<a href="https://pypi.python.org/pypi/gtfparse/">
+ <img src="https://img.shields.io/pypi/v/gtfparse.svg?maxAge=1000" alt="PyPI" />
+</a>
+
+gtfparse
+========
+Parsing tools for GTF (gene transfer format) files.
+
+# Example usage
+
+## Parsing all rows of a GTF file into a Pandas DataFrame
+
+```python
+from gtfparse import read_gtf
+
+# returns GTF with essential columns such as "feature", "seqname", "start", "end"
+# alongside the names of any optional keys which appeared in the attribute column
+df = read_gtf("gene_annotations.gtf")
+
+# filter DataFrame to gene entries on chrY
+df_genes = df[df["feature"] == "gene"]
+df_genes_chrY = df_genes[df_genes["seqname"] == "Y"]
+```
+
+
+## Getting gene FPKM values from a StringTie GTF file
+
+```python
+from gtfparse import read_gtf
+
+df = read_gtf(
+ "Transcripts.gtf",
+ column_converters={"FPKM": float})
+
+gene_fpkms = {
+ gene_name: fpkm
+ for (gene_name, fpkm, feature)
+ in zip(df["seqname"], df["FPKM"], df["feature"])
+ if feature == "gene"
+}
+```
+
+
=====================================
gtfparse/__init__.py
=====================================
@@ -16,7 +16,6 @@ from .required_columns import REQUIRED_COLUMNS
from .parsing_error import ParsingError
from .read_gtf import read_gtf, parse_gtf, parse_gtf_and_expand_attributes
-__version__ = "1.2.1"
__all__ = [
"expand_attribute_strings",
=====================================
gtfparse/attribute_parsing.py
=====================================
@@ -10,11 +10,9 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
import logging
from collections import OrderedDict
-
-from six.moves import intern
+from sys import intern
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
=====================================
gtfparse/create_missing_features.py
=====================================
@@ -10,7 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
import logging
from collections import OrderedDict
=====================================
gtfparse/parsing_error.py
=====================================
@@ -10,8 +10,5 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
-
class ParsingError(Exception):
pass
=====================================
gtfparse/read_gtf.py
=====================================
@@ -10,12 +10,10 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
import logging
from os.path import exists
-from six import string_types
-from six.moves import intern
+from sys import intern
import numpy as np
import pandas as pd
@@ -86,8 +84,7 @@ def parse_gtf(
names=REQUIRED_COLUMNS,
skipinitialspace=True,
skip_blank_lines=True,
- error_bad_lines=True,
- warn_bad_lines=True,
+ on_bad_lines="error",
chunksize=chunksize,
engine="c",
dtype={
@@ -201,14 +198,15 @@ def read_gtf(
chunksize : int
"""
- if isinstance(filepath_or_buffer, string_types) and not exists(filepath_or_buffer):
+ if type(filepath_or_buffer) is str and not exists(filepath_or_buffer):
raise ValueError("GTF file does not exist: %s" % filepath_or_buffer)
if expand_attribute_column:
result_df = parse_gtf_and_expand_attributes(
filepath_or_buffer,
chunksize=chunksize,
- restrict_attribute_columns=usecols)
+ restrict_attribute_columns=usecols,
+ features=features)
else:
result_df = parse_gtf(result_df, features=features)
=====================================
gtfparse/required_columns.py
=====================================
@@ -10,8 +10,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from __future__ import print_function, division, absolute_import
-
"""
Columns of a GTF file:
=====================================
gtfparse/version.py
=====================================
@@ -0,0 +1 @@
+__version__ = "1.3.0"
\ No newline at end of file
=====================================
setup.py
=====================================
@@ -28,7 +28,7 @@ except Exception as e:
print(e)
print("Failed to open %s" % readme_path)
-with open('gtfparse/__init__.py', 'r') as f:
+with open('gtfparse/version.py', 'r') as f:
version = re.search(
r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
f.read(),
View it on GitLab: https://salsa.debian.org/med-team/python-gtfparse/-/compare/b3f5490342d237407e9e15426241e62d78c86313...2401aa1f4cebd9079ed90bdd0127486dffd7b448
--
View it on GitLab: https://salsa.debian.org/med-team/python-gtfparse/-/compare/b3f5490342d237407e9e15426241e62d78c86313...2401aa1f4cebd9079ed90bdd0127486dffd7b448
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