comparison amplicon_analysis_pipeline.py @ 39:d19fca1c009c draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit c3970ae16b02774148dbf950880f07255734a9a8-dirty

38:7b2c40450792

            fp.write("---- %d: %s\n" % (ix,
                                        os.path.relpath(f,results_dir)))
    # Close output file
    if filen is not None:
        fp.close()

def find_executable(name):
    # Locate executable on PATH
    for p in os.environ['PATH'].split(os.pathsep):
        exe = os.path.normpath(
            os.path.abspath(os.path.join(p,name)))
        if os.path.isfile(exe) and os.access(exe,os.X_OK):
            return exe
    return None

if __name__ == "__main__":
    # Command line
    print "Amplicon analysis: starting"
    p = argparse.ArgumentParser()

        os.symlink(categories_file,"Categories.txt")
        print "-- made symlink to Categories.txt"

    # Link to FASTQs and construct Final_name.txt file
    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)))

39:d19fca1c009c

            fp.write("---- %d: %s\n" % (ix,
                                        os.path.relpath(f,results_dir)))
    # Close output file
    if filen is not None:
        fp.close()

if __name__ == "__main__":
    # Command line
    print "Amplicon analysis: starting"
    p = argparse.ArgumentParser()

        os.symlink(categories_file,"Categories.txt")
        print "-- made symlink to Categories.txt"

    # Link to FASTQs and construct Final_name.txt file
    sample_names = []
    print "-- making Final_name.txt"
    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 "   %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)))