gencodegenes 1.1.1__tar.gz → 1.1.4__tar.gz

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Files changed (34) hide show
  1. {gencodegenes-1.1.1/src/gencodegenes.egg-info → gencodegenes-1.1.4}/PKG-INFO +5 -3
  2. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/README.md +3 -2
  3. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/setup.py +1 -1
  4. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencodegenes/gencode.cpp +1022 -967
  5. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencodegenes/gencode.pyx +6 -6
  6. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencodegenes/transcript.cpp +536 -471
  7. {gencodegenes-1.1.1 → gencodegenes-1.1.4/src/gencodegenes.egg-info}/PKG-INFO +5 -3
  8. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gtf.cpp +31 -15
  9. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/LICENSE.txt +0 -0
  10. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/MANIFEST.in +0 -0
  11. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/pyproject.toml +0 -0
  12. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/setup.cfg +0 -0
  13. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencode.cpp +0 -0
  14. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencode.h +0 -0
  15. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencodegenes/__init__.py +0 -0
  16. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencodegenes/transcript.pxd +0 -0
  17. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencodegenes/transcript.pyx +0 -0
  18. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencodegenes/tx.cpp +0 -0
  19. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencodegenes/tx.h +0 -0
  20. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencodegenes.egg-info/SOURCES.txt +0 -0
  21. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencodegenes.egg-info/dependency_links.txt +0 -0
  22. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencodegenes.egg-info/requires.txt +0 -0
  23. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gencodegenes.egg-info/top_level.txt +0 -0
  24. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gtf.h +0 -0
  25. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gzstream/gzstream.C +0 -0
  26. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/gzstream/gzstream.h +0 -0
  27. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/tx.cpp +0 -0
  28. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/src/tx.h +0 -0
  29. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/tests/__init__.py +0 -0
  30. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/tests/data/example.grch38.fa +0 -0
  31. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/tests/data/example.grch38.gtf +0 -0
  32. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/tests/test_gencode.py +0 -0
  33. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/tests/test_sequence_methods.py +0 -0
  34. {gencodegenes-1.1.1 → gencodegenes-1.1.4}/tests/test_transcript.py +0 -0
{gencodegenes-1.1.1/src/gencodegenes.egg-info → gencodegenes-1.1.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: gencodegenes
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- Version: 1.1.1
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+ Version: 1.1.4
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  Summary: Package to load genes from GENCODE GTF files
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  Home-page: https://github.com/jeremymcrae/gencodegenes
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  Author: Jeremy McRae
@@ -12,12 +12,14 @@ Classifier: License :: OSI Approved :: MIT License
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  Requires-Python: >=3.8
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  Description-Content-Type: text/markdown
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  License-File: LICENSE.txt
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+ Requires-Dist: pyfaidx>=0.5.8
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  ### GENCODEGenes
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- This code loads genes from GENCODE GTF files into, groups transcripts by gene,
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- and provides methods for transcripts, so you can find CDS distances and sequences.
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+ This package loads genes from GENCODE GTF/GFF files, groups transcripts by gene,
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+ and provides methods for transcripts, so you can find exon coordinates, CDS
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+ distances and sequences.
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  ### Install
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  ```sh
{gencodegenes-1.1.1 → gencodegenes-1.1.4}/README.md RENAMED
@@ -1,8 +1,9 @@
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  ### GENCODEGenes
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- This code loads genes from GENCODE GTF files into, groups transcripts by gene,
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- and provides methods for transcripts, so you can find CDS distances and sequences.
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+ This package loads genes from GENCODE GTF/GFF files, groups transcripts by gene,
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+ and provides methods for transcripts, so you can find exon coordinates, CDS
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+ distances and sequences.
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  ### Install
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  ```sh
{gencodegenes-1.1.1 → gencodegenes-1.1.4}/setup.py RENAMED
@@ -112,7 +112,7 @@ setup(name="gencodegenes",
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  description='Package to load genes from GENCODE GTF files',
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  long_description=io.open('README.md', encoding='utf-8').read(),
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  long_description_content_type='text/markdown',
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- version="1.1.1",
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+ version="1.1.4",
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  author="Jeremy McRae",
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  author_email="jeremy.mcrae@gmail.com",
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  license="MIT",