comparison amplicon_analysis_pipeline.py @ 8:8292f8262a9d draft

planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit f72ff88ee11d09703bf38524dbb8026ee14bc3ef-dirty

7:1cd017d72920

            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()

        ref_database = "silva"
    elif args.use_homd:
        ref_database = "homd"
    else:
        ref_database = "gg"

    # Construct the pipeline command
    print "Amplicon analysis: constructing pipeline command"
    pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh")
    if args.forward_pcr_primer:

8:8292f8262a9d

            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.join(name)
        if os.path.isfike(exe) os.access(exe,os.X_OK):
            return exe
    return None

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

        ref_database = "silva"
    elif args.use_homd:
        ref_database = "homd"
    else:
        ref_database = "gg"

    # Executables
    os.mkdir("bin")
    os.environ["PATH"] = os.path.abspath("bin") + \
                         os.pathsep + \
                         os.environ["PATH"])
    print "-- updated PATH: %s" % os.environ["PATH"]
    # Pipeline wants 'vsearch113' but bioconda version is just
    # 'vsearch'
    vsearch = find_executable("vsearch113")
    if vsearch is None:
        vsearch = find_executable("vsearch")
    if vsearch:
        os.symlink(vsearch,os.path.join("bin","vsearch113"))
        print "-- made symlink to %s" % vsearch
    else:
        sys.stderr.write("Missing 'vsearch[113]'\n")
    # Pipeline wants 'fasta-splitter.pl' but bioconda provides
    # 'fasta-splitter'
    fasta_splitter = find_executable("fasta-splitter.pl")
    if fasta_splitter is None:
        fasta_splitter = os.path.readlink(
            find_executable("fasta-splitter"))
    if fasta_splitter:
        os.symlink(vsearch,os.path.join("bin","fasta-splitter.pl"))
    else:
        sys.stderr.write("Missing 'fasta-splitter[.pl]'\n")

    # Construct the pipeline command
    print "Amplicon analysis: constructing pipeline command"
    pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh")
    if args.forward_pcr_primer: