Moved template file to proper location

flowcraft/templates/renamePE_samtoolsFASTQ.py

@@ -0,0 +1,144 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+renamePE_samtoolsFASTQ.py - Rename the fastq headers with PE terminations
+that were not include in samtools fastq command
+<https://github.com/miguelpmachado/pythonScripts>
+Copyright (C) 2017 Miguel Machado <mpmachado@medicina.ulisboa.pt>
+Last modified: January 10, 2017
+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 sys
+import time
+import argparse
+
+version = '0.1'
+
+
+def format_fastq_headers(in_fastq_1, in_fastq_2, outdir):
+    out_fastq_1 = os.path.join(outdir,
+                               '{0}.headersRenamed_1.fq'.format(os.path.splitext(os.path.basename(in_fastq_1))[0]))
+    out_fastq_2 = os.path.join(outdir,
+                               '{0}.headersRenamed_2.fq'.format(os.path.splitext(os.path.basename(in_fastq_2))[0]))
+    writer_in_fastq_1 = open(out_fastq_1, 'wt')
+    writer_in_fastq_2 = open(out_fastq_2, 'wt')
+    outfiles = [out_fastq_1, out_fastq_2]
+    with open(in_fastq_1, 'rtU') as reader_in_fastq_1, open(in_fastq_2, 'rtU') as reader_in_fastq_2:
+        plus_line = True
+        quality_line = True
+        number_reads = 0
+        for in_1, in_2 in zip(reader_in_fastq_1, reader_in_fastq_2):
+            if len(in_1) > 0:
+                in_1 = in_1.splitlines()[0]
+                in_2 = in_2.splitlines()[0]
+                if in_1.startswith('@') and plus_line and quality_line:
+                    if in_1 != in_2:
+                        sys.exit('The PE fastq files are not aligned properly!')
+                    in_1 += '/1' + '\n'
+                    in_2 += '/2' + '\n'
+                    writer_in_fastq_1.write(in_1)
+                    writer_in_fastq_2.write(in_2)
+                    plus_line = False
+                    quality_line = False
+                elif in_1.startswith('+') and not plus_line:
+                    in_1 += '\n'
+                    writer_in_fastq_1.write(in_1)
+                    writer_in_fastq_2.write(in_1)
+                    plus_line = True
+                elif plus_line and not quality_line:
+                    in_1 += '\n'
+                    in_2 += '\n'
+                    writer_in_fastq_1.write(in_1)
+                    writer_in_fastq_2.write(in_2)
+                    writer_in_fastq_1.flush()
+                    writer_in_fastq_2.flush()
+                    number_reads += 1
+                    quality_line = True
+                else:
+                    in_1 += '\n'
+                    in_2 += '\n'
+                    writer_in_fastq_1.write(in_1)
+                    writer_in_fastq_2.write(in_2)
+    return number_reads, outfiles
+
+
+def compression_type(file_to_test):
+    magic_dict = {'\x1f\x8b\x08': ['gzip', 'gunzip'], '\x42\x5a\x68': ['bzip2', 'bunzip2']}
+
+    max_len = max(len(x) for x in magic_dict)
+
+    with open(file_to_test, 'r') as reader:
+        file_start = reader.read(max_len)
+
+    for magic, filetype in list(magic_dict.items()):
+        if file_start.startswith(magic):
+            return filetype
+    return None
+
+
+def run_time(start_time):
+    end_time = time.time()
+    time_taken = end_time - start_time
+    hours, rest = divmod(time_taken, 3600)
+    minutes, seconds = divmod(rest, 60)
+    print('Runtime :' + str(hours) + 'h:' + str(minutes) + 'm:' + str(round(seconds, 2)) + 's')
+    return time_taken
+
+
+def main():
+    parser = argparse.ArgumentParser(prog='renamePE_samtoolsFASTQ.py',
+                                     description='Rename the fastq headers with PE terminations that were not include '
+                                                 'in samtools fastq command',
+                                     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('-1', '--fastq_1', type=argparse.FileType('r'), metavar='/path/to/input/file_1.fq',
+                                 help='Uncompressed fastq file containing mate 1 reads', required=True)
+    parser_required.add_argument('-2', '--fastq_2', type=argparse.FileType('r'), metavar='/path/to/input/file_2.fq',
+                                 help='Uncompressed fastq file containing mate 2 reads', required=True)
+
+    parser_optional_general = parser.add_argument_group('General facultative options')
+    parser_optional_general.add_argument('-o', '--outdir', type=str, metavar='/output/directory/',
+                                         help='Path for output directory', required=False, default='.')
+
+    args = parser.parse_args()
+
+    print('\n' + 'STARTING renamePE_samtoolsFASTQ.py' + '\n')
+    start_time = time.time()
+
+    fastq_files = [os.path.abspath(args.fastq_1.name), os.path.abspath(args.fastq_2.name)]
+
+    print('Check if files are compressed' + '\n')
+    for fastq in fastq_files:
+        if compression_type(fastq) is not None:
+            sys.exit('Compressed fastq files found')
+
+    outdir = os.path.abspath(args.outdir)
+    if not os.path.isdir(outdir):
+        os.makedirs(outdir)
+
+    print('Renaming fastq headers' + '\n')
+    number_reads, outfiles = format_fastq_headers(fastq_files[0], fastq_files[1], outdir)
+
+    print('It was written ' + str(number_reads) + ' read pairs in ' + str(outfiles) + ' files' + '\n')
+
+    print('\n' + 'END renamePE_samtoolsFASTQ.py')
+    time_taken = run_time(start_time)
+    del time_taken
+
+
+if __name__ == "__main__":
+    main()