diff scripts/ReMatCh/utils/convert_Ns_to_gaps.py @ 0:c6bab5103a14 draft

"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/utils/convert_Ns_to_gaps.py	Mon Mar 21 15:23:09 2022 +0000
@@ -0,0 +1,85 @@
+#!/usr/bin/env python3
+
+# -*- coding: utf-8 -*-
+
+"""
+convert_Ns_to_gaps.py - Convert the Ns into gaps
+<https://github.com/B-UMMI/ReMatCh/>
+
+Copyright (C) 2018 Miguel Machado <[e-mail]>
+
+Last modified: October 15, 2018
+
+This program 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.
+
+This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import os
+import argparse
+
+
+version = '0.2'
+
+
+def conversion(infile, outfile):
+    last_printed = 0
+    counter = 1
+    with open(infile, 'rtU') as reader:
+        with open(outfile, 'wt') as writer:
+            for line in reader:
+                line = line.rstrip('\r\n')
+                if line.startswith('>'):
+                    writer.write(line + '\n')
+                    if counter % 10 == 0:
+                        print('\n' + str(counter) + ' sequences already processed')
+                        last_printed = counter
+                    counter += 1
+                else:
+                    if len(line) > 0:
+                        line = line.replace('N', '-')
+                        writer.write(line + '\n')
+    if last_printed < counter:
+        print('\n' + str(counter - 1) + ' sequences already processed')
+
+
+def convert_n_2_gaps(args):
+    outdir = os.path.dirname(os.path.abspath(args.outfile))
+    if not os.path.isdir(outdir):
+        os.makedirs(outdir)
+
+    outfile = os.path.abspath(args.outfile)
+
+    infile = os.path.abspath(args.infile.name)
+
+    conversion(infile, outfile)
+
+
+def main():
+    parser = argparse.ArgumentParser(prog='convert_Ns_to_gaps.py', description='Convert the Ns into gaps',
+                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version))
+
+    parser_required = parser.add_argument_group('Required options')
+    parser_required.add_argument('-i', '--infile', type=argparse.FileType('r'), metavar='/path/to/input/file.fasta',
+                                 help='Path to the fasta file', required=True)
+    parser_required.add_argument('-o', '--outfile', type=str, metavar='/path/to/converted/output/file.fasta',
+                                 help='Converted output fasta file', required=True,
+                                 default='converted_Ns_to_gaps.fasta')
+
+    args = parser.parse_args()
+
+    convert_n_2_gaps(args)
+
+
+if __name__ == "__main__":
+    main()