comparison blast_to_scaffold.py @ 2:61731b911f4e draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit e67f150062f2076d0879bcdd3376ef53ba639d91

1:35e2e6452cf7

        '--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")
    args = the_parser.parse_args()
    return args
    
def blatnInfo (file):
    blastlist = []

            except KeyError:
                continue
        for i, nucleotide in enumerate(sequence):
            GuideDict[i+subjectStart] = nucleotide
            
def finalAssembly (GuideDict, outputfile):
    finalSeqList = []
    for keys in sorted(GuideDict):
        finalSeqList.append(GuideDict[keys])
    finalSequence = insert_newlines("".join(finalSeqList) )
    Out = open (outputfile, "w")
    print >> Out, ">Scaffold"
    print >> Out, 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)

if __name__ == "__main__":
    __main__()

2:61731b911f4e

        '--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 = []

            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")
    print >> Out, ">Scaffold_from_%s_guided_by_%s" % (prefix, suffix)
    print >> Out, 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__()