subsample_15M.py

from subprocess import Popen, PIPE


def call_process(command, new_dir=None):
    p = Popen(command, shell=True, stdout=PIPE, stderr=PIPE, cwd=new_dir)
    stdout, stderr = p.communicate()
    stdout = stdout.decode()
    return stdout


if __name__ == '__main__':
    subdirectory_list = ['pe_reads_01',
                         'pe_reads_02',
                         'pe_reads_03',
                         'pe_reads_04',
                         'pe_reads_05',
                         'pe_reads_06',
                         'pe_reads_07',
                         'pe_reads_08',
                         'pe_reads_09',
                         'pe_reads_10',
                         'pe_reads_11',
                         'pe_reads_12',
                         'pe_reads_13',
                         'pe_reads_14',
                         'pe_reads_15']
    print('')
    for subdir in subdirectory_list:
        print('In subdirectory {}'.format(subdir))
        print('Subsampling the forward read')
        call_process('seqtk sample -s100 skewer-trimmed-pair1.fastq 15000000 > subsamp-skewer-trimmed-pair1.fastq', subdir)
        print('Subsampling the reverse read')
        call_process('seqtk sample -s100 skewer-trimmed-pair2.fastq 15000000 > subsamp-skewer-trimmed-pair2.fastq', subdir)
        print('')