RNApolis 0.9.0__tar.gz → 0.9.1__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 (47) hide show
  1. {rnapolis-0.9.0/src/RNApolis.egg-info → rnapolis-0.9.1}/PKG-INFO +1 -1
  2. {rnapolis-0.9.0 → rnapolis-0.9.1}/setup.py +1 -1
  3. {rnapolis-0.9.0 → rnapolis-0.9.1/src/RNApolis.egg-info}/PKG-INFO +1 -1
  4. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/annotator.py +7 -2
  5. {rnapolis-0.9.0 → rnapolis-0.9.1}/LICENSE +0 -0
  6. {rnapolis-0.9.0 → rnapolis-0.9.1}/README.md +0 -0
  7. {rnapolis-0.9.0 → rnapolis-0.9.1}/pyproject.toml +0 -0
  8. {rnapolis-0.9.0 → rnapolis-0.9.1}/setup.cfg +0 -0
  9. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/RNApolis.egg-info/SOURCES.txt +0 -0
  10. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/RNApolis.egg-info/dependency_links.txt +0 -0
  11. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/RNApolis.egg-info/entry_points.txt +0 -0
  12. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/RNApolis.egg-info/requires.txt +0 -0
  13. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/RNApolis.egg-info/top_level.txt +0 -0
  14. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/adapter.py +0 -0
  15. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/aligner.py +0 -0
  16. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/clashfinder.py +0 -0
  17. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/common.py +0 -0
  18. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/component_A.csv +0 -0
  19. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/component_C.csv +0 -0
  20. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/component_G.csv +0 -0
  21. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/component_U.csv +0 -0
  22. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/metareader.py +0 -0
  23. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/mmcif_pdbx_v50.dic +0 -0
  24. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/molecule_filter.py +0 -0
  25. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/motif_extractor.py +0 -0
  26. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/parser.py +0 -0
  27. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/parser_v2.py +0 -0
  28. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/py.typed +0 -0
  29. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/rfam_folder.py +0 -0
  30. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/splitter.py +0 -0
  31. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/tertiary.py +0 -0
  32. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/tertiary_v2.py +0 -0
  33. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/transformer.py +0 -0
  34. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/unifier.py +0 -0
  35. {rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/util.py +0 -0
  36. {rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_adapter.py +0 -0
  37. {rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_annotator.py +0 -0
  38. {rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_bugfixes.py +0 -0
  39. {rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_common.py +0 -0
  40. {rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_metareader.py +0 -0
  41. {rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_molecule_filter.py +0 -0
  42. {rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_parser.py +0 -0
  43. {rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_quadruplexes.py +0 -0
  44. {rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_rfam_folder.py +0 -0
  45. {rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_tertiary.py +0 -0
  46. {rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_transformer.py +0 -0
  47. {rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_v2.py +0 -0
{rnapolis-0.9.0/src/RNApolis.egg-info → rnapolis-0.9.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: RNApolis
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- Version: 0.9.0
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+ Version: 0.9.1
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  Summary: A Python library containing RNA-related bioinformatics functions and classes
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  Home-page: https://github.com/tzok/rnapolis-py
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  Author: Tomasz Zok
{rnapolis-0.9.0 → rnapolis-0.9.1}/setup.py RENAMED
@@ -5,7 +5,7 @@ with open("README.md") as f:
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  setup(
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  name="RNApolis",
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- version="0.9.0",
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+ version="0.9.1",
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  packages=["rnapolis"],
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  package_dir={"": "src"},
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  author="Tomasz Zok",
{rnapolis-0.9.0 → rnapolis-0.9.1/src/RNApolis.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: RNApolis
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- Version: 0.9.0
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+ Version: 0.9.1
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  Summary: A Python library containing RNA-related bioinformatics functions and classes
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  Home-page: https://github.com/tzok/rnapolis-py
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  Author: Tomasz Zok
{rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/annotator.py RENAMED
@@ -838,10 +838,15 @@ def main():
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  file = handle_input_file(args.input)
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  structure3d = read_3d_structure(file, None)
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  base_interactions = extract_base_interactions(structure3d)
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- structure2d, dot_brackets, mapping = structure3d.extract_secondary_structure(
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- base_interactions, args.find_gaps, args.all_dot_brackets
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+ structure2d, mapping = structure3d.extract_secondary_structure(
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+ base_interactions, args.find_gaps
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  )
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+ if args.all_dot_brackets:
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+ dot_brackets = mapping.all_dot_brackets
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+ else:
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+ dot_brackets = [mapping.dot_bracket]
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+
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  handle_output_arguments(args, structure2d, dot_brackets, mapping, args.input)
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{rnapolis-0.9.0 → rnapolis-0.9.1}/LICENSE RENAMED
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{rnapolis-0.9.0 → rnapolis-0.9.1}/README.md RENAMED
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{rnapolis-0.9.0 → rnapolis-0.9.1}/pyproject.toml RENAMED
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{rnapolis-0.9.0 → rnapolis-0.9.1}/setup.cfg RENAMED
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{rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/py.typed RENAMED
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{rnapolis-0.9.0 → rnapolis-0.9.1}/src/rnapolis/util.py RENAMED
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{rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_adapter.py RENAMED
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{rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_common.py RENAMED
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{rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_parser.py RENAMED
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{rnapolis-0.9.0 → rnapolis-0.9.1}/tests/test_v2.py RENAMED
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