sequence_splitter_sh.py

import sys
import os

if __name__ == '__main__':

    handle = sys.argv[1]

    header = '\
#!/bin/sh \n\
#$ -S /bin/sh \n\
#$ -cwd \n\
#$ -V\n\
#$ -m e\n\
#$ -M ericmjl@mit.edu \n\
#$ -pe whole_nodes 1\n\
#############################################\n \n\
'

    def check_dirs(dirname):
        if dirname not in os.listdir(os.getcwd()):
            os.mkdir(dirname)
        else:
            pass

    check_dirs('shell_scripts')
    check_dirs('split_fasta')

    for segment in range(1, 9):
        with open('shell_scripts/sequence_splitter{0}.sh'.format(segment),
                  'w') as f:
            f.write(header)

            f.write('cd ..\n')

            f.write('python sequence_splitter.py {0} {1}'
                    .format(handle, segment))

    with open('shell_scripts/sequence_splitter.sh', 'w') as f:
        f.write(header)

        for segment in range(1, 9):
            f.write('qsub sequence_splitter{0}.sh\n'.format(segment))