RNApolis 0.4.12__py3-none-any.whl → 0.4.14__py3-none-any.whl

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.
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: RNApolis
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- Version: 0.4.12
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+ Version: 0.4.14
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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
@@ -2,16 +2,16 @@ rnapolis/annotator.py,sha256=_hsSX2VHFvIQ47l_EA7lwGFXLiVLbhFPEsOQzBKbjRk,22100
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  rnapolis/clashfinder.py,sha256=i95kp0o6OWNqmJDBr-PbsZd7RY2iJtBDr7QqolJSuAQ,8513
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  rnapolis/common.py,sha256=LY6Uz96Br8ki_gA8LpfatgtvVbt9jOTkwgagayqTgf8,31251
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  rnapolis/metareader.py,sha256=I1-cXc2YNBPwa3zihAnMTjEsAo79tEKzSmWu5yvN1Pk,2071
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- rnapolis/molecule_filter.py,sha256=F_xkAe7q2NZAaDpRaeikv-twUvbNflWdlLte7oFn2Ms,9130
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+ rnapolis/molecule_filter.py,sha256=_7zrF-AH56vXI4vhFtfaU9wr-X7aeOL6DsXbX6_9vPQ,9497
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  rnapolis/motif_extractor.py,sha256=Lfn1iEkhkP9eZD3GPEWNAfy00QO7QPCc8wM_XS1ory8,1147
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  rnapolis/parser.py,sha256=lHI6LyFbEEPdHOzbged1-Ov0tl6MpSungIPacip0Py0,15838
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  rnapolis/rfam_folder.py,sha256=SjiiyML_T1__saruFwSMJEoQ7Y55GIU8ktS8ZUn5-fw,11111
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  rnapolis/tertiary.py,sha256=6t9ZB4w33-5n_M3sns1RoFXCOTgVAgGH4WDNG5OG9Kg,23426
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  rnapolis/transformer.py,sha256=aC0nBmHHJf5TyLvBIV57Jj3tlwpvHbPo347opfAOlQA,3844
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  rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
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- RNApolis-0.4.12.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
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- RNApolis-0.4.12.dist-info/METADATA,sha256=fPrlpVrM83UYwPYwaeymBP7SeVLMv7XftCZOl7hUnes,54323
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- RNApolis-0.4.12.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
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- RNApolis-0.4.12.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
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- RNApolis-0.4.12.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
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- RNApolis-0.4.12.dist-info/RECORD,,
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+ RNApolis-0.4.14.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
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+ RNApolis-0.4.14.dist-info/METADATA,sha256=MY6ulJgbaM4qJggOEswGUArvP0IsIMBX-zeoebjqjzk,54323
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+ RNApolis-0.4.14.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
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+ RNApolis-0.4.14.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
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+ RNApolis-0.4.14.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
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+ RNApolis-0.4.14.dist-info/RECORD,,
@@ -21,6 +21,7 @@ ENTITY_POLY_TYPES = [
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  ]
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  CATEGORIES_WITH_ENTITY_ID = [
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+ ("entity", "id"),
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  ("atom_site", "label_entity_id"),
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  ("entity_keywords", "entity_id"),
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  ("entity_name_com", "entity_id"),
@@ -155,7 +156,9 @@ def select_category_by_id(
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  def filter_by_poly_types(
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- file_content: str, entity_poly_types: Iterable[str] = ["polyribonucleotide"]
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+ file_content: str,
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+ entity_poly_types: Iterable[str] = ["polyribonucleotide"],
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+ retain_categories: Iterable[str] = [],
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  ) -> str:
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  adapter = IoAdapterPy()
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@@ -186,13 +189,20 @@ def filter_by_poly_types(
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  obj = DataCategory(category, attributes, rows)
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  output.append(obj)
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+ for category in retain_categories:
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+ obj = data[0].getObj(category)
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+ if obj:
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+ output.append(obj)
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+
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  with tempfile.NamedTemporaryFile("rt+") as tmp:
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  adapter.writeFile(tmp.name, [output])
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  tmp.seek(0)
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  return tmp.read()
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- def filter_by_chains(file_content: str, chains: Iterable[str]) -> str:
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+ def filter_by_chains(
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+ file_content: str, chains: Iterable[str], retain_categories: Iterable[str] = []
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+ ) -> str:
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  """
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  Filter a PDBx/mmCIF file by chain IDs. The function returns a new PDBx/mmCIF file.
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@@ -227,6 +237,11 @@ def filter_by_chains(file_content: str, chains: Iterable[str]) -> str:
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  obj = DataCategory(category, attributes, rows)
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  output.append(obj)
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+ for category in retain_categories:
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+ obj = data[0].getObj(category)
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+ if obj:
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+ output.append(obj)
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+
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  with tempfile.NamedTemporaryFile("rt+") as tmp:
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  adapter.writeFile(tmp.name, [output])
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  tmp.seek(0)