comparison msp_split.py @ 5:f2683ec717fe draft default tip

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a164f06c09dc1614c2909c247ebf390aab433527-dirty

4:769ec2496d14

import os
import re
import csv
import math

def msp_split(i, o, n):
    spec_total = lcount('NAME', i)
    spec_lim = math.ceil(spec_total/float(n))
    spec_c = 0
    filelist = []
    header = ''
    print('spec_lim', spec_lim)

                    line = msp_in.readline()

                    if not line:
                        break  # end of file

                    if re.match('^NAME:.*$', line, re.IGNORECASE):
                        header = line
                        spec_c += 1
                    else:
                        msp_out.write(line)
                spec_c = 1 

    return filelist

def lcount(keyword, fname):
    with open(fname, 'r') as fin:

                                formatter_class=argparse.RawDescriptionHelpFormatter,
                                description='''split msp files''',
                                )

    p.add_argument('-i', dest='i', help='msp file', required=True)
    p.add_argument('-o', dest='o', help='out dir', required=True)
    p.add_argument('-n', dest='n',)


    args = p.parse_args() 

    if not os.path.exists(args.o):
        os.makedirs(args.o)
    print('in file', args.i)
    print('out dir', args.o)
    print('nm files', args.n)

    msp_split(args.i, args.o, int(args.n))


if __name__ == '__main__':
    main()

5:f2683ec717fe

import os
import re
import csv
import math

def msp_split(i, o, x, n):
    spec_total = lcount(x, i)
    spec_lim = math.ceil(spec_total/float(n))
    spec_c = 0
    filelist = []
    header = ''
    print('spec_lim', spec_lim)

                    line = msp_in.readline()

                    if not line:
                        break  # end of file

                    if re.match('^{}.*$'.format(x), line, re.IGNORECASE):
                        header = line
                        spec_c += 1
                    else:
                        msp_out.write(line)
                spec_c = 1

    return filelist

def lcount(keyword, fname):
    with open(fname, 'r') as fin:

                                formatter_class=argparse.RawDescriptionHelpFormatter,
                                description='''split msp files''',
                                )

    p.add_argument('-i', dest='i', help='msp file', required=True)
    p.add_argument('-x', dest='x', help='name', default='RECORD_TITLE:')
    p.add_argument('-o', dest='o', help='out dir', required=True)
    p.add_argument('-n', dest='n',)


    args = p.parse_args()

    if not os.path.exists(args.o):
        os.makedirs(args.o)
    print('in file', args.i)
    print('out dir', args.o)
    print('Name of starting value in MSP', args.x)
    print('nm files', args.n)

    msp_split(args.i, args.o, args.x, int(args.n))


if __name__ == '__main__':
    main()