RNApolis 0.4.11__py3-none-any.whl → 0.4.13__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.
- {RNApolis-0.4.11.dist-info → RNApolis-0.4.13.dist-info}/METADATA +1 -1
- {RNApolis-0.4.11.dist-info → RNApolis-0.4.13.dist-info}/RECORD +7 -7
- rnapolis/molecule_filter.py +85 -29
- {RNApolis-0.4.11.dist-info → RNApolis-0.4.13.dist-info}/LICENSE +0 -0
- {RNApolis-0.4.11.dist-info → RNApolis-0.4.13.dist-info}/WHEEL +0 -0
- {RNApolis-0.4.11.dist-info → RNApolis-0.4.13.dist-info}/entry_points.txt +0 -0
- {RNApolis-0.4.11.dist-info → RNApolis-0.4.13.dist-info}/top_level.txt +0 -0
@@ -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=
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rnapolis/molecule_filter.py,sha256=1TDEIy2rgWXXqXxI21vjaElWExCFZlmCHWxwCfNehaM,9152
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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.
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RNApolis-0.4.
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RNApolis-0.4.
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RNApolis-0.4.
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RNApolis-0.4.
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RNApolis-0.4.
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RNApolis-0.4.13.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
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RNApolis-0.4.13.dist-info/METADATA,sha256=wzV8Xvo09Qv02NfCKaLTID2Sm9k07aKsSZzqVWaNwf8,54323
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RNApolis-0.4.13.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
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RNApolis-0.4.13.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
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RNApolis-0.4.13.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
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RNApolis-0.4.13.dist-info/RECORD,,
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rnapolis/molecule_filter.py
CHANGED
@@ -1,10 +1,11 @@
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#! /usr/bin/env python
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import argparse
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import tempfile
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from typing import List, Set, Tuple
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from typing import Iterable, List, Set, Tuple
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from mmcif.io.IoAdapterPy import IoAdapterPy
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from mmcif.io.PdbxReader import DataCategory, DataContainer
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from rnapolis.util import handle_input_file
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# Source: https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_entity_poly.type.html
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@@ -20,6 +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"),
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@@ -153,38 +155,63 @@ def select_category_by_id(
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return attributes, rows
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def
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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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) -> str:
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adapter = IoAdapterPy()
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with tempfile.NamedTemporaryFile("rt+") as f:
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f.write(file_content)
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f.seek(0)
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data = adapter.readFile(f.name)
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entity_ids = select_ids(
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data, "entity_poly", "type", "entity_id", set(entity_poly_types)
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)
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action="append",
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default=[],
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asym_ids = select_ids(data, "struct_asym", "entity_id", "id", entity_ids)
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auth_asym_ids = select_ids(
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data, "atom_site", "label_asym_id", "auth_asym_id", asym_ids
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)
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parser.add_argument("path", help="path to a PDBx/mmCIF file")
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args = parser.parse_args()
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file = handle_input_file(args.path)
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adapter = IoAdapterPy()
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data = adapter.readFile(file.name)
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output = DataContainer("rnapolis")
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asym_ids
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asym_ids = select_ids(data, "struct_asym", "entity_id", "id", entity_ids)
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for table, ids in (
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(CATEGORIES_WITH_ENTITY_ID, entity_ids),
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(CATEGORIES_WITH_ASYM_ID, asym_ids),
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(CATEGORIES_WITH_AUTH_ASYM_ID, auth_asym_ids),
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):
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for category, field_name in table:
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attributes, rows = select_category_by_id(data, category, field_name, ids)
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if attributes and rows:
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obj = DataCategory(category, attributes, rows)
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output.append(obj)
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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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"""
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Filter a PDBx/mmCIF file by chain IDs. The function returns a new PDBx/mmCIF file.
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Warning! The new file might contain more chains than provided in the `chains` argument.
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This is because the function filters by entity, so if you ask for chain "A",
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which is part of entity 1 having chains "A", "B" and "C", then you will get all three chains.
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"""
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adapter = IoAdapterPy()
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with tempfile.NamedTemporaryFile("rt+") as f:
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f.write(file_content)
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f.seek(0)
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data = adapter.readFile(f.name)
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output = DataContainer("rnapolis")
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entity_ids = select_ids(data, "struct_asym", "id", "entity_id", set(chains))
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asym_ids = set(chains)
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auth_asym_ids = select_ids(
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data, "atom_site", "label_asym_id", "auth_asym_id", asym_ids
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)
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obj = DataCategory(category, attributes, rows)
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output.append(obj)
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with tempfile.NamedTemporaryFile() as tmp:
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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 main():
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parser = argparse.ArgumentParser()
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parser.add_argument(
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"--type",
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help="a type of molecule to select, you can provide this argument multiple times (default: polyribonucleotide)",
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action="append",
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default=["polyribonucleotide"],
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choices=ENTITY_POLY_TYPES,
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)
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parser.add_argument(
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"--chain",
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help="a chain ID (label_asym_id) to select, you can provide this argument multiple times (if provided, it overrides the --type argument)",
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action="append",
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default=[],
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)
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parser.add_argument("path", help="path to a PDBx/mmCIF file")
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args = parser.parse_args()
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file = handle_input_file(args.path)
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if args.chain:
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print(filter_by_chains(file.read(), args.chain))
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elif args.type:
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print(filter_by_poly_types(file.read(), args.type))
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else:
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parser.print_help()
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if __name__ == "__main__":
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