[med-svn] [Git][med-team/python-gtfparse][upstream] New upstream version 1.3.0+ds
Mohd Bilal (@rmb)
gitlab at salsa.debian.org
Sun Dec 4 13:01:07 GMT 2022
Mohd Bilal pushed to branch upstream at Debian Med / python-gtfparse
Commits:
22228862 by Mohammed Bilal at 2022-12-04T10:54:30+00:00
New upstream version 1.3.0+ds
- - - - -
12 changed files:
- + LICENSE
- PKG-INFO
- README.md
- 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"
}
```
=====================================
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/-/commit/2222886259dfd9a6f03887118aab4a98d17e5c3f
--
View it on GitLab: https://salsa.debian.org/med-team/python-gtfparse/-/commit/2222886259dfd9a6f03887118aab4a98d17e5c3f
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