annotate 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

#!/usr/bin/python
import argparse
from collections import defaultdict


def Parser():
    the_parser = argparse.ArgumentParser()
    the_parser.add_argument('--blast', action="store", type=str,
                            help="Path to the blast output\
                                  (tabular format, 12 column)")
    the_parser.add_argument('--sequences', action="store", type=str,
                            help="Path to the fasta file with blasted\
                                  sequences")
    the_parser.add_argument('--fastaOutput', action="store", type=str,
                            help="fasta output file of blast hits")
    the_parser.add_argument('--tabularOutput', action="store", type=str,
                            help="tabular output file of blast analysis")
    the_parser.add_argument('--flanking', action="store", type=int,
                            help="number of flanking nucleotides\
                                  added to the hit sequences")
    the_parser.add_argument('--mode', action="store",
                            choices=["verbose", "short"], type=str,
                            help="reporting (verbose) or not reporting (short)\
                                  oases contigs")
    the_parser.add_argument('--filter_relativeCov', action="store", type=float,
                            default=0,
                            help="filter out relative coverages\
                                  below the specified ratio (float number)")
    the_parser.add_argument('--filter_maxScore', action="store", type=float,
                            default=0, help="filter out best BitScores below\
                                             the specified float number")
    the_parser.add_argument('--filter_meanScore', action="store", type=float,
                            default=0,
                            help="filter out mean BitScores below the\
                                  specified float number")
    the_parser.add_argument('--filter_term_in', action="store", type=str,
                            default="",
                            help="select the specified term in the\
                                  subject list")
    the_parser.add_argument('--filter_term_out', action="store", type=str,
                            default="",
                            help="exclude the specified term from\
                                  the subject list")
    the_parser.add_argument('--al_sequences', action="store", type=str,
                            help="sequences that have been blast aligned")
    the_parser.add_argument('--un_sequences', action="store", type=str,
                            help="sequences that have not been blast aligned")
    the_parser.add_argument('--dataset_name', action="store", type=str,
                            default="",
                            help="the name of the dataset that has been parsed,\
                                  to be reported in the output")
    args = the_parser.parse_args()
    if not all((args.sequences, args.blast, args.fastaOutput,
                args.tabularOutput)):
        the_parser.error('argument(s) missing, call the\
                         -h option of the script')
    if not args.flanking:
        args.flanking = 0
    return args


def median(lst):
    lst = sorted(lst)
    if len(lst) < 1:
            return None
    if len(lst) % 2 == 1:
            return lst[((len(lst)+1)/2)-1]
    if len(lst) % 2 == 0:
            return float(sum(lst[(len(lst)/2)-1:(len(lst)/2)+1]))/2.0


def mean(lst):
    if len(lst) < 1:
        return 0
    return sum(lst) / float(len(lst))


def getfasta(fastafile):
    fastadic = {}
    for line in open(fastafile):
        if line[0] == ">":
            header = line[1:-1]
            fastadic[header] = ""
        else:
            fastadic[header] += line
    for header in fastadic:
        fastadic[header] = "".join(fastadic[header].split("\n"))
    return fastadic


def insert_newlines(string, every=60):
    lines = []
    for i in range(0, len(string), every):
        lines.append(string[i:i+every])
    return '\n'.join(lines)


def getblast(blastfile):
    '''blastinfo [0]	Percentage of identical matches
       blastinfo [1]	Alignment length
       blastinfo [2]	Number of mismatches
       blastinfo [3]	Number of gap openings
       blastinfo [4]	Start of alignment in query
       blastinfo [5]	End of alignment in query
       blastinfo [6]	Start of alignment in subject (database hit)
       blastinfo [7]	End of alignment in subject (database hit)
       blastinfo [8]	Expectation value (E-value)
       blastinfo [9]	Bit score
       blastinfo [10]	Subject length
                        (NEED TO BE SPECIFIED WHEN RUNNING BLAST) '''
    blastdic = defaultdict(dict)
    for line in open(blastfile):
        fields = line[:-1].split("\t")
        transcript = fields[0]
        subject = fields[1]
        # blastinfo[0]
        blastinfo = [float(fields[2])]
        # blastinfo[1:8] insets 1 to 7
        blastinfo = blastinfo + [int(i) for i in fields[3:10]]
        # blastinfo[8] E-value remains as a string type
        blastinfo.append(fields[10])
        # blastinfo[9] Bit score
        blastinfo.append(float(fields[11]))
        # blastinfo[10] Subject length MUST BE RETRIEVED
        # THROUGH A 13 COLUMN BLAST OUTPUT
        blastinfo.append(int(fields[12]))
        try:
            blastdic[subject][transcript].append(blastinfo)
        except Exception:
            blastdic[subject][transcript] = [blastinfo]
    return blastdic


def getseq(fastadict, transcript, up, down, orientation="direct"):
    def reverse(seq):
        revdict = {"A": "T", "T": "A", "G": "C", "C": "G", "N": "N"}
        revseq = [revdict[i] for i in seq[::-1]]
        return "".join(revseq)
    pickseq = fastadict[transcript][up-1:down]
    if orientation == "direct":
        return pickseq
    else:
        return reverse(pickseq)


def subjectCoverage(fastadict, blastdict, subject,
                    QueriesFlankingNucleotides=0):
    SubjectCoverageList = []
    HitDic = {}
    bitScores = []
    for transcript in blastdict[subject]:
        prefix = "%s--%s_" % (subject, transcript)
        hitNumber = 0
        for hit in blastdict[subject][transcript]:
            hitNumber += 1
            suffix = "hit%s_IdMatch=%s,AligLength=%s,E-val=%s" % (hitNumber,
                                                                  hit[0],
                                                                  hit[1],
                                                                  hit[8])
            # query coverage by a hit is in hit[4:6]
            HitDic[prefix+suffix] = GetHitSequence(fastadict, transcript,
                                                   hit[4], hit[5],
                                                   QueriesFlankingNucleotides)
            # subject coverage by a hit is in hit[6:8]
            SubjectCoverageList += range(min([hit[6], hit[7]]),
                                         max([hit[6], hit[7]]) + 1)
            bitScores.append(hit[9])
            # always the same value for a given subject. Stupid but simple
            subjectLength = hit[10]
    TotalSubjectCoverage = len(set(SubjectCoverageList))
    RelativeSubjectCoverage = TotalSubjectCoverage/float(subjectLength)
    return (HitDic, subjectLength, TotalSubjectCoverage,
            RelativeSubjectCoverage, max(bitScores), mean(bitScores))


def GetHitSequence(fastadict, FastaHeader, leftCoordinate, rightCoordinate,
                   FlankingValue):
    if rightCoordinate > leftCoordinate:
        polarity = "direct"
    else:
        polarity = "reverse"
        leftCoordinate, rightCoordinate = rightCoordinate, leftCoordinate
    if leftCoordinate - FlankingValue > 0:
        leftCoordinate -= FlankingValue
    else:
        leftCoordinate = 1
    return getseq(fastadict, FastaHeader, leftCoordinate, rightCoordinate,
                  polarity)


def outputParsing(dataset_name, F, Fasta, results, Xblastdict, fastadict,
                  filter_relativeCov=0, filter_maxScore=0, filter_meanScore=0,
                  filter_term_in="", filter_term_out="", mode="verbose"):
    def filter_results(results, filter_relativeCov=0, filter_maxScore=0,
                       filter_meanScore=0, filter_term_in="",
                       filter_term_out=""):
        for subject in results.keys():
            if results[subject][
                       "RelativeSubjectCoverage"] < filter_relativeCov:
                del results[subject]
                continue
            if results[subject]["maxBitScores"] < filter_maxScore:
                del results[subject]
                continue
            if results[subject]["meanBitScores"] < filter_meanScore:
                del results[subject]
                continue
            if filter_term_in in subject:
                pass
            else:
                del results[subject]
                continue
            if filter_term_out and filter_term_out in subject:
                del results[subject]
                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",
                                                        "EndSubject",
                                                        "%QueryHitCov",
                                                        "E-value",
                                                        "BitScore"))
        for subject in sorted(results,
                              key=lambda x: results[x]["meanBitScores"],
                              reverse=True):
            F.write(" \n# %s\n" % subject)
            F.write("# Suject Length: %s\n" %
                    results[subject]["subjectLength"])
            F.write("# Total Subject Coverage: %s\n" %
                    results[subject]["TotalCoverage"])
            F.write("# Relative Subject Coverage: %s\n" %
                    results[subject]["RelativeSubjectCoverage"])
            F.write("# Best Bit Score: %s\n" % results[subject][
                                                       "maxBitScores"])
            F.write("# Mean Bit Score: %s\n" % results[subject][
                                                       "meanBitScores"])
            for header in results[subject]["HitDic"]:
                Fasta.write(">%s\n%s\n" % (header,
                                           insert_newlines(results[subject][
                                                                   "HitDic"][
                                                                   header])))
            Fasta.write("\n")  # final carriage return for the sequence
            for transcript in Xblastdict[subject]:
                transcriptSize = float(len(fastadict[transcript]))
                for hit in Xblastdict[subject][transcript]:
                    percentIdentity = hit[0]
                    alignLenght = hit[1]
                    subjectStart = hit[6]
                    subjectEnd = hit[7]
                    queryCov = "%.1f" % (abs(hit[5]-hit[4])/transcriptSize*100)
                    Eval, BitScore = hit[8], hit[9]
                    info = [transcript] + [percentIdentity, alignLenght,
                                           subjectStart, subjectEnd, queryCov,
                                           Eval, BitScore]
                    info = [str(i) for i in info]
                    info = "\t".join(info)
                    F.write("%s\n" % info)
    else:
        F.write("--- %s ---\n" % dataset_name)
        F.write("# subject\tsubject length\tTotal Subject Coverage\tRelative\
                 Subject Coverage\tBest Bit Score\tMean Bit Score\n")
        for subject in sorted(results,
                              key=lambda x: results[x]["meanBitScores"],
                              reverse=True):
            line = []
            line.append(subject)
            line.append(results[subject]["subjectLength"])
            line.append(results[subject]["TotalCoverage"])
            line.append(results[subject]["RelativeSubjectCoverage"])
            line.append(results[subject]["maxBitScores"])
            line.append(results[subject]["meanBitScores"])
            line = [str(i) for i in line]
            F.write("%s\n" % "\t".join(line))
            for header in results[subject]["HitDic"]:
                Fasta.write(">%s\n%s\n" % (header,
                                           insert_newlines(
                                               results[subject][
                                                       "HitDic"][header])))
            Fasta.write("\n")  # final carriage return for the sequence
    F.close()
    Fasta.close()
    return blasted_transcripts


def dispatch_sequences(fastadict, blasted_transcripts, matched_sequences,
                       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


def __main__():
    args = Parser()
    fastadict = getfasta(args.sequences)
    Xblastdict = getblast(args.blast)
    results = defaultdict(dict)
    for subject in Xblastdict:
        results[subject]["HitDic"], results[subject]["subjectLength"], results[
            subject]["TotalCoverage"], results[subject][
            "RelativeSubjectCoverage"], results[subject][
            "maxBitScores"], results[subject][
            "meanBitScores"] = subjectCoverage(fastadict, Xblastdict, subject,
                                               args.flanking)
    blasted_transcripts = outputParsing(
        args.dataset_name, args.tabularOutput,
        args.fastaOutput, results, Xblastdict, fastadict,
        filter_relativeCov=args.filter_relativeCov,
        filter_maxScore=args.filter_maxScore,
        filter_meanScore=args.filter_meanScore,
        filter_term_in=args.filter_term_in,
        filter_term_out=args.filter_term_out, mode=args.mode)
    dispatch_sequences(fastadict, blasted_transcripts, args.al_sequences,
                       args.un_sequences)


if __name__ == "__main__":
    __main__()