generate sample_list according to info.txt and list.txt

get_sample_list.py

#!/usr/bin/env python
#-*- coding: utf-8 -*-

def get_sample_list(infofile, listfile):
    sampledict = {}
    with open(infofile) as f:
        for line in f:
            sampleid,novoid = line.strip().split('\t')[2:4]
            sampledict[novoid] = sampleid
    
    with open('sample_list', 'w') as out:
        out.write('Ori_lane\tPatientID\tSampleID\tLibID\tNovoID\tIndex\tPath\n')
        with open(listfile) as f:
            for line in f:
                linelist = line.strip().split('\t')
                lane = linelist[0]
                libid = linelist[9]
                novoid = linelist[4]
                index = linelist[10]
                path = linelist[18]
                patientid = sampleid = sampledict[novoid]
                out.write('{}\t{}\t{}\t{}\t{}\t{}\t{}\n'.format(lane, patientid, sampleid, libid, novoid, index, path))


if __name__ == '__main__':
    import sys
    if len(sys.argv) < 3:
        print "Usage python %s <info.txt> <list.txt>" % sys.argv[0]
        exit(1)
        
    get_sample_list(sys.argv[1], sys.argv[2])