gtfparse 2.5.0__tar.gz → 2.6.2__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (25) hide show
  1. {gtfparse-2.5.0 → gtfparse-2.6.2}/PKG-INFO +7 -7
  2. {gtfparse-2.5.0 → gtfparse-2.6.2}/README.md +1 -3
  3. {gtfparse-2.5.0 → gtfparse-2.6.2}/gtfparse/__init__.py +4 -5
  4. {gtfparse-2.5.0 → gtfparse-2.6.2}/gtfparse/read_gtf.py +6 -2
  5. {gtfparse-2.5.0 → gtfparse-2.6.2}/gtfparse.egg-info/PKG-INFO +7 -7
  6. gtfparse-2.6.2/gtfparse.egg-info/requires.txt +3 -0
  7. {gtfparse-2.5.0 → gtfparse-2.6.2}/pyproject.toml +9 -1
  8. gtfparse-2.6.2/requirements.txt +3 -0
  9. {gtfparse-2.5.0 → gtfparse-2.6.2}/tests/test_ensembl_gtf.py +1 -1
  10. {gtfparse-2.5.0 → gtfparse-2.6.2}/tests/test_read_stringtie_gtf.py +1 -1
  11. {gtfparse-2.5.0 → gtfparse-2.6.2}/tests/test_refseq_gtf.py +1 -1
  12. gtfparse-2.5.0/gtfparse.egg-info/requires.txt +0 -2
  13. gtfparse-2.5.0/requirements.txt +0 -2
  14. {gtfparse-2.5.0 → gtfparse-2.6.2}/LICENSE +0 -0
  15. {gtfparse-2.5.0 → gtfparse-2.6.2}/gtfparse/attribute_parsing.py +0 -0
  16. {gtfparse-2.5.0 → gtfparse-2.6.2}/gtfparse/create_missing_features.py +0 -0
  17. {gtfparse-2.5.0 → gtfparse-2.6.2}/gtfparse/parsing_error.py +0 -0
  18. {gtfparse-2.5.0 → gtfparse-2.6.2}/gtfparse.egg-info/SOURCES.txt +0 -0
  19. {gtfparse-2.5.0 → gtfparse-2.6.2}/gtfparse.egg-info/dependency_links.txt +0 -0
  20. {gtfparse-2.5.0 → gtfparse-2.6.2}/gtfparse.egg-info/top_level.txt +0 -0
  21. {gtfparse-2.5.0 → gtfparse-2.6.2}/setup.cfg +0 -0
  22. {gtfparse-2.5.0 → gtfparse-2.6.2}/tests/test_create_missing_features.py +0 -0
  23. {gtfparse-2.5.0 → gtfparse-2.6.2}/tests/test_expand_attributes.py +0 -0
  24. {gtfparse-2.5.0 → gtfparse-2.6.2}/tests/test_multiple_values_for_tag_attribute.py +0 -0
  25. {gtfparse-2.5.0 → gtfparse-2.6.2}/tests/test_parse_gtf_lines.py +0 -0
{gtfparse-2.5.0 → gtfparse-2.6.2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.1
1
+ Metadata-Version: 2.4
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  Name: gtfparse
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- Version: 2.5.0
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+ Version: 2.6.2
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  Summary: Parsing library for extracting data frames of genomic features from GTF files
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  Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
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  Project-URL: Homepage, https://github.com/openvax/gtfparse
@@ -15,12 +15,12 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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  Requires-Python: >=3.7
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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- Requires-Dist: polars<0.21.0,>=0.20.2
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- Requires-Dist: pyarrow<14.1.0,>=14.0.2
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+ Requires-Dist: polars>=0.20.2
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+ Requires-Dist: pyarrow>=18.0.0
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+ Requires-Dist: pandas>=2.1.0
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+ Dynamic: license-file
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22
 
21
- <!--
22
- [![Build Status](https://travis-ci.org/openvax/gtfparse.svg?branch=master)](https://travis-ci.org/openvax/gtfparse)
23
- -->
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+ [![Tests](https://github.com/openvax/gtfparse/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/gtfparse/actions/workflows/tests.yml)
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  [![Coverage Status](https://coveralls.io/repos/openvax/gtfparse/badge.svg?branch=master&service=github)](https://coveralls.io/github/openvax/gtfparse?branch=master)
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  <a href="https://pypi.python.org/pypi/gtfparse/">
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  <img src="https://img.shields.io/pypi/v/gtfparse.svg?maxAge=1000" alt="PyPI" />
{gtfparse-2.5.0 → gtfparse-2.6.2}/README.md RENAMED
@@ -1,6 +1,4 @@
1
- <!--
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- [![Build Status](https://travis-ci.org/openvax/gtfparse.svg?branch=master)](https://travis-ci.org/openvax/gtfparse)
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- -->
1
+ [![Tests](https://github.com/openvax/gtfparse/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/gtfparse/actions/workflows/tests.yml)
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  [![Coverage Status](https://coveralls.io/repos/openvax/gtfparse/badge.svg?branch=master&service=github)](https://coveralls.io/github/openvax/gtfparse?branch=master)
5
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  <a href="https://pypi.python.org/pypi/gtfparse/">
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  <img src="https://img.shields.io/pypi/v/gtfparse.svg?maxAge=1000" alt="PyPI" />
{gtfparse-2.5.0 → gtfparse-2.6.2}/gtfparse/__init__.py RENAMED
@@ -14,20 +14,19 @@ from .attribute_parsing import expand_attribute_strings
14
14
  from .create_missing_features import create_missing_features
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  from .parsing_error import ParsingError
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  from .read_gtf import (
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- read_gtf,
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+ read_gtf,
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  parse_gtf,
19
- parse_gtf_pandas,
20
- parse_gtf_and_expand_attributes,
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+ parse_gtf_pandas,
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+ parse_gtf_and_expand_attributes,
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  REQUIRED_COLUMNS,
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  )
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24
- __version__ = "2.5.0"
24
+ __version__ = "2.6.2"
25
25
 
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  __all__ = [
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  "__version__",
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  "expand_attribute_strings",
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  "create_missing_features",
30
-
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  "parse_gtf_and_expand_attributes",
32
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  "REQUIRED_COLUMNS",
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  "ParsingError",
{gtfparse-2.5.0 → gtfparse-2.6.2}/gtfparse/read_gtf.py RENAMED
@@ -101,15 +101,18 @@ def parse_with_polars_lazy(
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  separator="\t",
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  comment_prefix="#",
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  null_values=".",
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- dtypes=DEFAULT_COLUMN_DTYPES)
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+ schema_overrides=DEFAULT_COLUMN_DTYPES)
105
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  try:
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  df = polars.read_csv(
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  filepath_or_buffer,
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  new_columns=REQUIRED_COLUMNS,
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  **kwargs).lazy()
110
- except polars.ShapeError:
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+ except polars.exceptions.ShapeError:
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  raise ParsingError("Wrong number of columns")
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+ # Drop empty lines that may appear as all-null rows
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+ df = df.filter(polars.col("seqname").is_not_null())
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+
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  df = df.with_columns([
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  polars.col("frame").fill_null(0),
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  polars.col("attribute").str.replace_all('"', "'")
@@ -299,6 +302,7 @@ def read_gtf(
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  valid_columns = [c for c in usecols if c in column_names]
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  result_df = result_df[valid_columns]
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+ result = None
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  if result_type == "pandas":
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  result = result_df
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  elif result_type == "polars":
{gtfparse-2.5.0 → gtfparse-2.6.2}/gtfparse.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.1
1
+ Metadata-Version: 2.4
2
2
  Name: gtfparse
3
- Version: 2.5.0
3
+ Version: 2.6.2
4
4
  Summary: Parsing library for extracting data frames of genomic features from GTF files
5
5
  Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
6
6
  Project-URL: Homepage, https://github.com/openvax/gtfparse
@@ -15,12 +15,12 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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  Requires-Python: >=3.7
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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- Requires-Dist: polars<0.21.0,>=0.20.2
19
- Requires-Dist: pyarrow<14.1.0,>=14.0.2
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+ Requires-Dist: polars>=0.20.2
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+ Requires-Dist: pyarrow>=18.0.0
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+ Requires-Dist: pandas>=2.1.0
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+ Dynamic: license-file
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22
 
21
- <!--
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- [![Build Status](https://travis-ci.org/openvax/gtfparse.svg?branch=master)](https://travis-ci.org/openvax/gtfparse)
23
- -->
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+ [![Tests](https://github.com/openvax/gtfparse/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/gtfparse/actions/workflows/tests.yml)
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  [![Coverage Status](https://coveralls.io/repos/openvax/gtfparse/badge.svg?branch=master&service=github)](https://coveralls.io/github/openvax/gtfparse?branch=master)
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  <a href="https://pypi.python.org/pypi/gtfparse/">
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  <img src="https://img.shields.io/pypi/v/gtfparse.svg?maxAge=1000" alt="PyPI" />
gtfparse-2.6.2/gtfparse.egg-info/requires.txt ADDED
@@ -0,0 +1,3 @@
1
+ polars>=0.20.2
2
+ pyarrow>=18.0.0
3
+ pandas>=2.1.0
{gtfparse-2.5.0 → gtfparse-2.6.2}/pyproject.toml RENAMED
@@ -24,4 +24,12 @@ packages = ["gtfparse"]
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  [project.urls]
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  "Homepage" = "https://github.com/openvax/gtfparse"
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- "Bug Tracker" = "https://github.com/openvax/gtfparse"
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+ "Bug Tracker" = "https://github.com/openvax/gtfparse"
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+
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+ [tool.ruff.lint]
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+ select = ["E", "F"]
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+ ignore = ["F821", "E501", "F841", "E731", "E741", "E722", "E721"]
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+
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+ [tool.ruff.lint.per-file-ignores]
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+ "__init__.py" = ["F401"]
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+ "test*/*" = ["F401"]
gtfparse-2.6.2/requirements.txt ADDED
@@ -0,0 +1,3 @@
1
+ polars>=0.20.2
2
+ pyarrow>=18.0.0
3
+ pandas>=2.1.0
{gtfparse-2.5.0 → gtfparse-2.6.2}/tests/test_ensembl_gtf.py RENAMED
@@ -1,6 +1,6 @@
1
- from data import data_path
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1
  from gtfparse import read_gtf
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2
 
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+ from .data import data_path
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  ENSEMBL_GTF_PATH = data_path("ensembl_grch37.head.gtf")
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6
 
{gtfparse-2.5.0 → gtfparse-2.6.2}/tests/test_read_stringtie_gtf.py RENAMED
@@ -1,5 +1,5 @@
1
1
  from gtfparse import read_gtf
2
- from data import data_path
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+ from .data import data_path
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3
 
4
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  B16_GTF_PATH = data_path("B16.stringtie.head.gtf")
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5
 
{gtfparse-2.5.0 → gtfparse-2.6.2}/tests/test_refseq_gtf.py RENAMED
@@ -1,5 +1,5 @@
1
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  from gtfparse import read_gtf
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- from data import data_path
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+ from .data import data_path
3
3
 
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  REFSEQ_GTF_PATH = data_path("refseq.ucsc.small.gtf")
5
5
 
gtfparse-2.5.0/gtfparse.egg-info/requires.txt DELETED
@@ -1,2 +0,0 @@
1
- polars<0.21.0,>=0.20.2
2
- pyarrow<14.1.0,>=14.0.2
gtfparse-2.5.0/requirements.txt DELETED
@@ -1,2 +0,0 @@
1
- polars>=0.20.2,<0.21.0
2
- pyarrow>=14.0.2,<14.1.0
{gtfparse-2.5.0 → gtfparse-2.6.2}/LICENSE RENAMED
File without changes
{gtfparse-2.5.0 → gtfparse-2.6.2}/setup.cfg RENAMED
File without changes