added splitDomains fn

greedyFAS/splitDomains.py

@@ -0,0 +1,85 @@
+#!/bin/env python
+
+#######################################################################
+# Copyright (C) 2024 Vinh Tran
+#
+# This file is part of FAS.
+#
+#  FAS is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  FAS is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with FAS.  If not, see <http://www.gnu.org/licenses/>.
+#
+#######################################################################
+
+
+import os
+from pathlib import Path
+import sys
+import argparse
+from pkg_resources import get_distribution
+
+
+def split_domainFile(domain_file, outdir, idlist):
+    # get list of input protein ids (if given):
+    ids = ''
+    if os.path.exists(idlist):
+        with open(idlist, 'r') as idf:
+            ids = idf.read().splitlines()
+    # parse domain file
+    domain_dict = {}
+    header = ''
+    if os.path.exists(domain_file):
+        with open(domain_file, 'r') as df:
+            for l in df.read().splitlines():
+                if l.startswith('#'):
+                    header = l
+                else:
+                    id = l.split('#')[0]
+                    if (len(ids) > 0 and id in ids) or len(ids) == 0:
+                        if not id in domain_dict:
+                            domain_dict[id] = [l]
+                        else:
+                            domain_dict[id].append(l)
+    else:
+        sys.exit(f'ERROR: {domain_file} not found!')
+    # write single domain files to outdir
+    if len(domain_dict) > 0:
+        if not os.path.exists(os.path.abspath(outdir)):
+            Path(os.path.abspath(outdir)).mkdir(parents = True, exist_ok = True)
+        for id in domain_dict:
+            with open(f'{outdir}/{id}.domains', 'w') as o:
+                o.write('%s\n%s' % (header, '\n'.join(domain_dict[id])))
+
+
+def main():
+    version = get_distribution('greedyFAS').version
+    parser = argparse.ArgumentParser(description='You are running FAS version ' + str(version) + '.' +
+                                     ' This script is used to split a domain file into individual file for each protein',
+                                     epilog="For more information on certain options, please refer to the wiki pages "
+                                            "on github: https://github.com/BIONF/FAS/wiki")
+    required = parser.add_argument_group('required arguments')
+    optional = parser.add_argument_group('optional arguments')
+    required.add_argument("-i", "--input", default='.', type=str, required=True,
+                          help="Input domain file")
+    required.add_argument("-o", "--outdir", default='.', type=str, required=True,
+                          help="Output directory")
+    optional.add_argument("--idlist", default='', type=str, required=False,
+                          help="File containing list of protein IDs that need to be splitted")
+    args = parser.parse_args()
+
+
+    domain_dict = split_domainFile(args.input, args.outdir, args.idlist)
+    print(f'DONE! Output files saved in {os.path.abspath(args.outdir)}')
+
+
+if __name__ == '__main__':
+    main()

setup.py

@@ -28,7 +28,7 @@
 
 setup(
     name='greedyFAS',
-    version='1.18.10',
+    version='1.18.11',
     python_requires='>=3.7.0',
     description='A tool to compare protein feature architectures',
     long_description=long_description,
@@ -58,6 +58,7 @@
                             'fas.runFdogFas = greedyFAS.fdogFAS:main',
                             'fas.calcComplexity = greedyFAS.complexityFAS:main',
                             'fas.getDomains = greedyFAS.domainFAS:main',
+                            'fas.splitDomains = greedyFAS.splitDomains:main',
                             'fas.splitAnno = greedyFAS.extractAnnoFAS:main',
                             'fas.disorder.predict = greedyFAS.disorderFAS.predict_disorder:main',
                             'fas.disorder.setup = greedyFAS.disorderFAS.install_aucpred:main',