comparison amplicon_analysis_pipeline.py @ 38:7b2c40450792 draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 601f7d1e21b25c583cc6e1a563029bab3f226921-dirty

37:e832be1635b4

    for line in message.split('\n'):
        sys.stderr.write("* %s%s *\n" % (line,' '*(width-len(line)-4)))
    sys.stderr.write("%s\n\n" % ('*'*width))

def clean_up_name(sample):
    # Remove trailing "_L[0-9]+_001" from Fastq
    # pair names
    split_name = sample.split('_')
    if split_name[-1] == "001":
        split_name = split_name[:-1]
    if split_name[-1].startswith('L'):
        try:
            int(split_name[-1][1:])

    sample_names = []
    with open("Final_name.txt",'w') as final_name:
        fastqs = iter(args.fastq_pairs)
        for sample_name,fqr1,fqr2 in zip(fastqs,fastqs,fastqs):
            sample_name = clean_up_name(sample_name)
            r1 = "%s_R1_.fastq" % sample_name
            r2 = "%s_R2_.fastq" % sample_name
            os.symlink(fqr1,r1)
            os.symlink(fqr2,r2)
            final_name.write("%s\n" % '\t'.join((r1,sample_name)))

38:7b2c40450792

    for line in message.split('\n'):
        sys.stderr.write("* %s%s *\n" % (line,' '*(width-len(line)-4)))
    sys.stderr.write("%s\n\n" % ('*'*width))

def clean_up_name(sample):
    # Remove extensions and trailing "_L[0-9]+_001" from
    # Fastq pair names
    sample_name = '.'.join(sample.split('.')[:1])
    split_name = sample_name.split('_')
    if split_name[-1] == "001":
        split_name = split_name[:-1]
    if split_name[-1].startswith('L'):
        try:
            int(split_name[-1][1:])

    sample_names = []
    with open("Final_name.txt",'w') as final_name:
        fastqs = iter(args.fastq_pairs)
        for sample_name,fqr1,fqr2 in zip(fastqs,fastqs,fastqs):
            sample_name = clean_up_name(sample_name)
            print "Cleaned up sample name: %s" % sample_name
            r1 = "%s_R1_.fastq" % sample_name
            r2 = "%s_R2_.fastq" % sample_name
            os.symlink(fqr1,r1)
            os.symlink(fqr2,r2)
            final_name.write("%s\n" % '\t'.join((r1,sample_name)))