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protein_name_strip #52

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8d4fc3b
protein_name_strip
amudhakumari Jan 21, 2025
15bfb93
-p argument removed
amudhakumari Jan 21, 2025
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2 changes: 0 additions & 2 deletions AddedAnnotations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,6 @@ def run(filename):
Example:
python AddedAnnotations.py -w '[{"/path/to/working/folder"}]'
-f '[{"/path/to/EMDB/header/files/folder"}]'
-p '[{"/path/to/PDBe/files/folder"}]'
--uniprot --CPX --component --model --weight --pmc --GO --interpro --pfam --pbdekb
--cath --scop --scop2 --scop2B --rfam
"""
Expand All @@ -142,7 +141,6 @@ def run(filename):
parser.add_argument("-h", "--help", action="help", help="Show this help message and exit.")
parser.add_argument('-w', '--workDir', type=Path, help="Main working directory path .")
parser.add_argument('-f', '--headerDir', type=Path, help="Directory path to the EMDB version 3.0 header files.")
parser.add_argument('-p', '--PDBeDir', type=Path, help="Directory path to the PDBe Complex portal mapping files.")
parser.add_argument('-t', '--threads', type=int, default=4, help="Number of threads.")
parser.add_argument('--json', type=Path, help="Path to release json file.")
parser.add_argument("--all", type=bool, nargs='?', const=True, default=False, help="Fetch all external resources.")
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4 changes: 2 additions & 2 deletions XMLParser.py
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Expand Up @@ -103,7 +103,7 @@ def read_xml(self):
supramolecule = Supramolecule(self.emdb_id, complex_id)
supramolecule.id = f"supra_{complex_id}" #TODO: Is this supra_ id used anywhere?
supramolecule.type = "supra" #TODO: Where is it being used?
complex_name = complex_tag.find('name').text
complex_name = complex_tag.find('name').text.replace('\t', ' ').strip()
supramolecule.name = f"{complex_name}_{complex_id}"
self.supramolecules.append(supramolecule)

Expand All @@ -119,7 +119,7 @@ def read_xml(self):
sample_id = protein_tag.attrib['macromolecule_id']
protein = Protein(self.emdb_id, sample_id)
protein.pdb = self.models
protein.sample_name = protein_tag.find('name').text
protein.sample_name = protein_tag.find('name').text.replace('\t', ' ').strip()
if sample_id in protein_cpx:
protein.sample_complexes = list(protein_cpx[sample_id])
if protein_tag.find('number_of_copies') is not None:
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