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

"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/ReMatCh/utils/combine_alignment_consensus.py	Mon Mar 21 15:23:09 2022 +0000
@@ -0,0 +1,120 @@
+#!/usr/bin/env python3
+
+# -*- coding: utf-8 -*-
+
+"""
+combine_alignment_consensus.py - Combine the alignment consensus
+sequences from ReMatCh first run by reference sequences into single
+files
+<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
+import time
+import sys
+
+version = '0.2'
+
+
+def concatenate_files(input_files_list, outdir):
+    all_executed_printed = False
+    for x, input_file in enumerate(input_files_list):
+        sample = os.path.basename(input_file).rsplit('.', 2)[0]
+        with open(input_file, 'rtU') as reader:
+            writer = None
+            for line in reader:
+                line = line.rstrip('\r\n')
+                if line.startswith('>'):
+                    file_output = os.path.join(outdir, line[1:] + '.fasta')
+                    if writer is not None:
+                        writer.flush()
+                        writer.close()
+                    if os.path.isfile(file_output):
+                        writer = open(file_output, 'at')
+                    else:
+                        writer = open(file_output, 'wt')
+                    writer.write('>' + sample + '\n')
+                else:
+                    if len(line) > 0:
+                        writer.write(line + '\n')
+            writer.flush()
+            writer.close()
+
+        if (x + 1) % 100 == 0:
+            print('\n' + str(round((float(x + 1) / len(input_files_list)) * 100, 2)) + '% of IDs already processed')
+            all_executed_printed = True
+    if not all_executed_printed:
+        print('\n' + str(round((float(x + 1) / len(input_files_list)) * 100, 2)) + '% of IDs already processed')
+
+
+def combine_alignment_consensus(args):
+    outdir = os.path.abspath(args.outdir)
+    if not os.path.isdir(outdir):
+        os.makedirs(outdir)
+
+    outdir = os.path.join(outdir, 'combine_alignment_consensus_' + time.strftime("%Y%m%d-%H%M%S"), '')
+    os.makedirs(outdir)
+
+    workdir = os.path.abspath(args.workdir)
+
+    alignment_files = []
+    directories = [d for d in os.listdir(workdir) if
+                   not d.startswith('.') and
+                   os.path.isdir(os.path.join(workdir, d, ''))]
+    for sample_dir in directories:
+        sample_dir_path = os.path.join(workdir, sample_dir, '')
+        files = [f for f in os.listdir(sample_dir_path) if
+                 not f.startswith('.') and
+                 os.path.isfile(os.path.join(sample_dir_path, f))]
+        for file_found in files:
+            if file_found.endswith('.alignment.fasta'):
+                file_found_path = os.path.join(sample_dir_path, file_found)
+                alignment_files.append(file_found_path)
+
+    if len(alignment_files) > 0:
+        concatenate_files(alignment_files, outdir)
+    else:
+        sys.exit('No ReMatCh alignment.fasta files were found!')
+
+
+def main():
+    parser = argparse.ArgumentParser(prog='combine_alignment_consensus.py',
+                                     description='Combine the alignment consensus sequences from ReMatCh first run by'
+                                                 ' reference sequences into single'
+                                                 ' files', 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('-w', '--workdir', type=str, metavar='/path/to/rematch/working/directory/',
+                                 help='Path to the directory where ReMatCh was running', required=True)
+
+    parser_optional_general = parser.add_argument_group('General facultative options')
+    parser_optional_general.add_argument('-o', '--outdir', type=str, metavar='/path/to/output/directory/',
+                                         help='Path to the directory where the combined sequence files will stored',
+                                         required=False, default='.')
+
+    args = parser.parse_args()
+
+    combine_alignment_consensus(args)
+
+
+if __name__ == "__main__":
+    main()