view blastx_to_scaffold.py @ 0:bdf781f2658b draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d

#!/usr/bin/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 Parser():
    the_parser = argparse.ArgumentParser(
        description="Generate DNA scaffold from blastx alignment of Contigs")
    the_parser.add_argument('--sequences', action="store", type=str,
                            help="input sequence file in fasta format")
    the_parser.add_argument('--blastx-tab', dest="blastx_tab", action="store",
                            type=str, help="13-columns tabular blastx output")
    the_parser.add_argument('--output', action="store", type=str,
                            help="output file path, fasta format")
    args = the_parser.parse_args()
    return args


def __main__():
    args = Parser()
    protLenght = int(open(args.blastx_tab, "r").readline().split("\t")[12])
    BlastxOutput = open(args.blastx_tab, "r")
    Contigs = open(args.sequences, "r")
    ContigsDict = {}
    protScaffold = {}
    for line in Contigs:
        if line[0] == ">":
            header = line[1:-1]
            ContigsDict[header] = ""
        else:
            ContigsDict[header] += line[:-1]
    protScaffold = dict([(i, "NNN") for i in range(1, protLenght+1)])
    for line in BlastxOutput:
        fields = line[:-1].split("\t")
        queryStart = int(fields[6])
        queryStop = int(fields[7])
        subjectStart = int(fields[8])
        subjectStop = int(fields[9])
        seqHeader = fields[0]
        sequence = ContigsDict[seqHeader]
        for i in range(subjectStart, subjectStop):
            del protScaffold[i]
        protScaffold[subjectStop] = sequence[queryStart-1: queryStop]
    finalSeqList = []
    for i in sorted(protScaffold):
        finalSeqList.append(protScaffold[i])
    finalSequence = insert_newlines("".join(finalSeqList))
    Out = open(args.output, "w")
    Out.write(">Scaffold\n")
    Out.write("%s\n" % finalSequence)
    BlastxOutput.close()
    Contigs.close()
    Out.close()


if __name__ == "__main__":
    __main__()