comparison BlastParser_and_hits.py @ 2:36103afa0934 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits commit 22ac2287a510708784dec78647afea4eff658f02

1:9beb85dba280

                continue
        return results

    F = open(F, "w")
    Fasta = open(Fasta, "w")
    blasted_transcripts = []
    filter_results(results, filter_relativeCov, filter_maxScore,
                   filter_meanScore, filter_term_in, filter_term_out)
    for subject in results:
        for transcript in Xblastdict[subject]:
            blasted_transcripts.append(transcript)
    blasted_transcripts = list(set(blasted_transcripts))
    if mode == "verbose":
        F.write("--- %s ---\n" % dataset_name)
        F.write("# %s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ("SeqId", "%Identity",
                                                        "AlignLength",
                                                        "StartSubject",

                       unmatched_sequences):
    '''to output the sequences that matched and did not matched in the blast'''
    F_matched = open(matched_sequences, "w")
    F_unmatched = open(unmatched_sequences, "w")
    for transcript in fastadict:
        if transcript in blasted_transcripts:
            ''''list of blasted_transcripts is generated
            by the outputParsing function'''
            F_matched.write(">%s\n%s\n" % (transcript, insert_newlines(
                                           fastadict[transcript])))
        else:
            F_unmatched.write(">%s\n%s\n" % (transcript, insert_newlines(
                                             fastadict[transcript])))
    F_matched.close()
    F_unmatched.close()
    return

2:36103afa0934

                continue
        return results

    F = open(F, "w")
    Fasta = open(Fasta, "w")
    blasted_transcripts = dict()
    filter_results(results, filter_relativeCov, filter_maxScore,
                   filter_meanScore, filter_term_in, filter_term_out)
    for subject in results:
        for transcript in Xblastdict[subject]:
            blasted_transcripts[transcript] = ">%s\n%s\n" % (transcript,
                                                             insert_newlines(
                                                                 fastadict[
                                                                     transcript
                                                                     ]))
    if mode == "verbose":
        F.write("--- %s ---\n" % dataset_name)
        F.write("# %s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ("SeqId", "%Identity",
                                                        "AlignLength",
                                                        "StartSubject",

                       unmatched_sequences):
    '''to output the sequences that matched and did not matched in the blast'''
    F_matched = open(matched_sequences, "w")
    F_unmatched = open(unmatched_sequences, "w")
    for transcript in fastadict:
        try:
            F_matched.write(blasted_transcripts[transcript])
        except KeyError:
            F_unmatched.write(">%s\n%s\n" % (transcript, insert_newlines(
                                            fastadict[transcript])))
    F_matched.close()
    F_unmatched.close()
    return