annotate blast_to_scaffold.py @ 0:7d96b28eec49 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1

#!/usr/bin/env python
import argparse


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 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 Parser():
    the_parser = argparse.ArgumentParser(
        description="Generate DNA scaffold from blastn or tblastx alignment\
                     of Contigs")
    the_parser.add_argument('--sequences', action="store", type=str,
                            help="input sequence file in fasta format")
    the_parser.add_argument('--guideSequence', action="store", type=str,
                            help="the reference sequence to guide the scaffold\
                                  assembly in fasta format")
    the_parser.add_argument('--blast-tab', dest="blast_tab", action="store",
                            type=str,
                            help="13-columns tabular blastn or tblastx output")
    the_parser.add_argument('--output', action="store", type=str,
                            help="output file path, fasta format")
    the_parser.add_argument('--scaffold_prefix', action="store", type=str,
                            help="the prefix that will be used for the header\
                                  of the fasta scaffold")
    the_parser.add_argument('--scaffold_suffix', action="store", type=str,
                            help="the sufix that will be used for the header\
                                  of the fasta scaffold")
    args = the_parser.parse_args()
    return args


def blatnInfo(file):
    blastlist = []
    with open(file, "r") as f:
        for line in f:
            minilist = []
            fields = line.rstrip().split()
            minilist.append(fields[0])
            minilist.extend(fields[6:10])
            blastlist.append(minilist)
    blastlist.sort(key=lambda x: x[3], reverse=True)
    return blastlist


def myContigs(file):
    Contigs = {}
    with open(file, "r") as f:
        for line in f:
            if line[0] == ">":
                header = line[1:-1]
                Contigs[header] = ""
            else:
                Contigs[header] += line[:-1]
    return Contigs


def myGuide(file):
    Guide = {}
    coordinate = 0
    with open(file, "r") as f:
        for line in f:
            if line[0] == ">":
                continue
            else:
                for nucleotide in line[:-1]:
                    coordinate += 1
                    Guide[coordinate] = nucleotide.lower()
    return Guide


def updateGuide(blastlist, GuideDict, ContigsDict):
    '''
    the blastlist object is a list of list with
    element [0] : name of the blasted Contig
    element [1] : queryStart of the alignment to the reference
    element [2] = queryStop of the alignment to the reference
    element [3] : subjectStart of the alignment to the reference
    element [4] = subjectStop of the alignment to the reference
    '''
    for fields in blastlist:
        seqHeader = fields[0]
        queryStart = int(fields[1])
        queryStop = int(fields[2])
        subjectStart = int(fields[3])
        subjectStop = int(fields[4])
        if subjectStart > subjectStop:
            subjectStart, subjectStop = subjectStop, subjectStart
            orientation = "reverse"
        else:
            orientation = "direct"
        sequence = getseq(ContigsDict, seqHeader, queryStart, queryStop,
                          orientation)
        for i in range(subjectStart, subjectStop+1):
            try:
                del GuideDict[i]
            except KeyError:
                continue
        for i, nucleotide in enumerate(sequence):
            GuideDict[i+subjectStart] = nucleotide


def finalAssembly(GuideDict, outputfile, prefix, suffix):
    finalSeqList = []
    for keys in sorted(GuideDict):
        finalSeqList.append(GuideDict[keys])
    finalSequence = insert_newlines("".join(finalSeqList))
    Out = open(outputfile, "w")
    Out.write(">Scaffold_from_%s_guided_by_%s\n" % (prefix, suffix))
    Out.write("%s\n" % finalSequence)
    Out.close()


def __main__():
    args = Parser()
    ContigsDict = myContigs(args.sequences)
    GuideDict = myGuide(args.guideSequence)
    blastlist = blatnInfo(args.blast_tab)
    updateGuide(blastlist, GuideDict, ContigsDict)
    finalAssembly(GuideDict, args.output, args.scaffold_prefix,
                  args.scaffold_suffix)


if __name__ == "__main__":
    __main__()