batch_merge.py

#!/usr/bin/python
# filename: batch_merge.py

###########################################################################
#
# Copyright (c) 2013 Bryan Briney.  All rights reserved.
# Copyright (c) 2021 Rinat Mukhometzianov.
# @version: 1.0.0
# @author: Bryan Briney, Rinat Mukhometzianov
# @props: IgBLAST team (http://www.ncbi.nlm.nih.gov/igblast/igblast.cgi)
# @license: MIT (http://opensource.org/licenses/MIT) 
#
###########################################################################


import os
import glob
import shutil
import argparse

import pandaseq

parser = argparse.ArgumentParser("Batch merging of paired-end reads with PANDAseq")
parser.add_argument('-i', '--in', dest='input', required=True, help="The input directory, containing paired FASTQ files"
                                                                    " (uncompressed or gzip compressed). Required.")
parser.add_argument('-o', '--out', dest='output', required=True,
                    help="The output directory, will contain merged FASTA files. Required.")
parser.add_argument('-n', '--nextseq', dest='nextseq', default=False, action='store_true',
                    help="Use flag if run was performed on a NextSeq sequencer.")
args = parser.parse_args()


def make_direc(d):
    if not os.path.exists(d):
        os.mkdir(d)


def remove_direc(d):
    shutil.rmtree(d)


def list_files(d):
    return sorted([f for f in glob.glob(d + '/*') if os.path.isfile(f)])


def bin_files(files):
    file_bins = {}
    for f in files:
        f_pre = '_'.join(os.path.basename(f).split('_')[:-1])
        if f_pre in file_bins:
            file_bins[f_pre].append(f)
        else:
            file_bins[f_pre] = [f, ]
    return file_bins


def concat(d):
    files = list_files(d)
    file_bins = bin_files(files)
    for file_bin in file_bins:
        outfile = os.path.join(args.output, '{}.fasta'.format(file_bin))
        with open(outfile, 'w') as o:
            for f in file_bins[file_bin]:
                with open(f) as i:
                    for line in i:
                        o.write(line)


def main():
    make_direc(args.output)
    if args.nextseq:
        temp = os.path.join(args.output, 'temp')
        make_direc(temp)
        o = temp
    else:
        o = args.output
    pandaseq.run(args.input, o, args.nextseq)
    if args.nextseq:
        print('')
        print('Concatenating NextSeq lane files for each sample...')
        concat(o)
        remove_direc(o)
        print('Done.')
        print('')


if __name__ == '__main__':
    main()