comparison blastxml_to_gapped_gff3.py @ 17:4c201a3d4755 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66

16:1fe91657bfd6

            "BLASTP": "protein_match",
        }.get(record.application, "match")

        recid = record.query
        if " " in recid:
            recid = recid[0: recid.index(" ")]

        rec = SeqRecord(Seq("ACTG"), id=recid)
        for idx_hit, hit in enumerate(record.alignments):
            for idx_hsp, hsp in enumerate(hit.hsps):
                qualifiers = {

                    "sbjct_end",
                ):
                    qualifiers["blast_" + prop] = getattr(hsp, prop, None)

                desc = hit.title.split(" >")[0]
                qualifiers["description"] = desc[desc.index(" "):]

                # This required a fair bit of sketching out/match to figure out
                # the first time.
                #
                # the match_start location must account for queries and

    prev = 0
    fq = ""
    fm = ""
    fs = ""
    for position in re.finditer("-", query):
        fq += query[prev: position.start()]
        fm += match[prev: position.start()]
        fs += subject[prev: position.start()]
        prev = position.start() + 1
    fq += query[prev:]
    fm += match[prev:]
    fs += subject[prev:]

        "--trim",
        action="store_true",
        help="Trim blast hits to be only as long as the parent feature",
    )
    parser.add_argument(
        "--trim_end", action="store_true", help="Cut blast results off at end of gene"
    )
    parser.add_argument("--include_seq", action="store_true", help="Include sequence")
    args = parser.parse_args()

    for rec in blastxml2gff3(**vars(args)):

17:4c201a3d4755

            "BLASTP": "protein_match",
        }.get(record.application, "match")

        recid = record.query
        if " " in recid:
            recid = recid[0 : recid.index(" ")]

        rec = SeqRecord(Seq("ACTG"), id=recid)
        for idx_hit, hit in enumerate(record.alignments):
            for idx_hsp, hsp in enumerate(hit.hsps):
                qualifiers = {

                    "sbjct_end",
                ):
                    qualifiers["blast_" + prop] = getattr(hsp, prop, None)

                desc = hit.title.split(" >")[0]
                qualifiers["description"] = desc[desc.index(" ") :]

                # This required a fair bit of sketching out/match to figure out
                # the first time.
                #
                # the match_start location must account for queries and

    prev = 0
    fq = ""
    fm = ""
    fs = ""
    for position in re.finditer("-", query):
        fq += query[prev : position.start()]
        fm += match[prev : position.start()]
        fs += subject[prev : position.start()]
        prev = position.start() + 1
    fq += query[prev:]
    fm += match[prev:]
    fs += subject[prev:]

        "--trim",
        action="store_true",
        help="Trim blast hits to be only as long as the parent feature",
    )
    parser.add_argument(
        "--trim_end",
        action="store_true",
        help="Cut blast results off at end of gene",
    )
    parser.add_argument("--include_seq", action="store_true", help="Include sequence")
    args = parser.parse_args()

    for rec in blastxml2gff3(**vars(args)):