<div dir="ltr">Hi,<div>I wrote a script which should changes IDs in a GFF3 file. Unfortunately, the below script has two problems.<br><br>1. It attaches the new ID to `Parent` which leads that `Parent` contains the old and new id. How is it possible to keep only the new one?<br>2. How is it possible to access the chromosome name?<br><br>This how to run the script `<i>python renameIDgff3.py --gff3 braker_utr.gff3 --prefix ACTG --output braker_utr-newID.gff3</i>`<br><br>  <i>  #!/usr/bin/python3<br>    import click<br>    from BCBio.GFF import GFFExaminer<br>    from BCBio import GFF<br>    <br>    @click.command()<br>    @click.option('--gff3', help="Provide GFF3 file", required=True)<br>    @click.option('--prefix', help="e.g. ASSCTG", required=True)<br>    @click.option('--output', help="Keep GFF3 file", required=True)<br>    def run(gff3, prefix, output):<br>        print("Hello")<br>        with open(output, "w") as out_handle:<br>            for rec in GFF.parse(gff3):<br>                <br>                for count, feature in enumerate(rec.features):<br>                    print("count", count)<br>                    print(feature)<br>                    print(feature.qualifiers.get("Name"))<br>                    print(feature.sub_features)<br>                    print(feature.sub_features[0].qualifiers.get("Name"))<br>                    print("!!!!change")<br>                    feature.qualifiers["ID"] = prefix + str(count).zfill(6)<br>                   <br>    <br>                    print(feature.sub_features[0].qualifiers["ID"])<br>                    id_extension =  feature.sub_features[0].qualifiers["ID"][0].split('.')[1]<br>                    feature.sub_features[0].qualifiers["ID"] = prefix + str(count).zfill(6) + '.' + id_extension<br>                    print(feature.sub_features[0].qualifiers["Parent"])<br>                    print("-----------")<br>    <br>                GFF.write([rec], out_handle)<br>    <br>    if __name__ == '__main__':<br>        run()<br></i><br>Input file:<br>    <br> <i>   NbV1Ch08       AUGUSTUS        gene    7015    29794   0.01    -       .       ID=g1;<br>    NbV1Ch08  AUGUSTUS        mRNA    7015    29794   0.01    -       .       ID=g1.t1;Parent=g1<br>    NbV1Ch08      AUGUSTUS        transcription_end_site  7015    7015    .       -       .       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        three_prime_utr 7015    8531    0.2     -       .       ID=g1.t1.3UTR1;Parent=g1.t1<br>    NbV1Ch08     AUGUSTUS        exon    7015    8747    .       -       .       ID=g1.t1.exon1;Parent=g1.t1;<br>    NbV1Ch08    AUGUSTUS        stop_codon      8532    8534    .       -       0       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        CDS     8532    8747    0.31    -       0       ID=g1.t1.CDS1;Parent=g1.t1<br>    NbV1Ch08      AUGUSTUS        intron  8748    9191    0.49    -       .       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        CDS     9192    9342    0.66    -       1       ID=g1.t1.CDS2;Parent=g1.t1<br>    NbV1Ch08      AUGUSTUS        exon    9192    9342    .       -       .       ID=g1.t1.exon2;Parent=g1.t1;<br>    NbV1Ch08    AUGUSTUS        intron  9343    9915    0.58    -       .       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        CDS     9916    10006   0.71    -       2       ID=g1.t1.CDS3;Parent=g1.t1<br>    NbV1Ch08      AUGUSTUS        exon    9916    10006   .       -       .       ID=g1.t1.exon3;Parent=g1.t1;<br>    NbV1Ch08    AUGUSTUS        intron  10007   10101   0.74    -       .       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        CDS     10102   10201   0.78    -       0       ID=g1.t1.CDS4;Parent=g1.t1<br>    NbV1Ch08      AUGUSTUS        exon    10102   10201   .       -       .       ID=g1.t1.exon4;Parent=g1.t1;<br>    NbV1Ch08    AUGUSTUS        intron  10202   10712   0.8     -       .       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        CDS     10713   11107   0.11    -       2       ID=g1.t1.CDS5;Parent=g1.t1<br>    NbV1Ch08      AUGUSTUS        exon    10713   11107   .       -       .       ID=g1.t1.exon5;Parent=g1.t1;<br>    NbV1Ch08    AUGUSTUS        intron  11108   11569   0.07    -       .       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        CDS     11570   12151   0.09    -       2       ID=g1.t1.CDS6;Parent=g1.t1<br>    NbV1Ch08      AUGUSTUS        exon    11570   12151   .       -       .       ID=g1.t1.exon6;Parent=g1.t1;<br>    NbV1Ch08    AUGUSTUS        intron  12152   12588   0.34    -       .       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        CDS     12589   12717   0.39    -       2       ID=g1.t1.CDS7;Parent=g1.t1<br>    NbV1Ch08      AUGUSTUS        exon    12589   12717   .       -       .       ID=g1.t1.exon7;Parent=g1.t1;<br>    NbV1Ch08    AUGUSTUS        intron  12718   12789   0.42    -       .       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        CDS     12790   13075   0.39    -       0       ID=g1.t1.CDS8;Parent=g1.t1<br>    NbV1Ch08      AUGUSTUS        exon    12790   13075   .       -       .       ID=g1.t1.exon8;Parent=g1.t1;<br>    NbV1Ch08    AUGUSTUS        intron  13076   14832   0.51    -       .       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        CDS     14833   15009   0.39    -       0       ID=g1.t1.CDS9;Parent=g1.t1<br>    NbV1Ch08      AUGUSTUS        exon    14833   15009   .       -       .       ID=g1.t1.exon9;Parent=g1.t1;<br>    NbV1Ch08    AUGUSTUS        intron  15010   15278   0.59    -       .       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        CDS     15279   15415   0.56    -       2       ID=g1.t1.CDS10;Parent=g1.t1<br>    NbV1Ch08     AUGUSTUS        exon    15279   15415   .       -       .       ID=g1.t1.exon10;Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        intron  15416   15487   0.58    -       .       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        CDS     15488   15612   0.96    -       1       ID=g1.t1.CDS11;Parent=g1.t1<br>    NbV1Ch08     AUGUSTUS        exon    15488   15612   .       -       .       ID=g1.t1.exon11;Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        intron  15613   15706   0.96    -       .       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        CDS     15707   15957   0.98    -       0       ID=g1.t1.CDS12;Parent=g1.t1<br>    NbV1Ch08     AUGUSTUS        exon    15707   15958   .       -       .       ID=g1.t1.exon12;Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        start_codon     15955   15957   .       -       0       Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        five_prime_utr  15958   15958   0.99    -       .       ID=g1.t1.5UTR1;Parent=g1.t1<br>    NbV1Ch08     AUGUSTUS        five_prime_utr  27458   28250   0.37    -       .       ID=g1.t1.5UTR2;Parent=g1.t1<br>    NbV1Ch08     AUGUSTUS        exon    27458   28250   .       -       .       ID=g1.t1.exon13;Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        five_prime_utr  29272   29794   0.08    -       .       ID=g1.t1.5UTR3;Parent=g1.t1<br>    NbV1Ch08     AUGUSTUS        exon    29272   29794   .       -       .       ID=g1.t1.exon14;Parent=g1.t1;<br>    NbV1Ch08   AUGUSTUS        transcription_start_site        29794   29794   .       -       .       Parent=g1.t1;<br></i><br>Output file:<br><br>   <i> ##gff-version 3<br>    ##sequence-region NbV1Ch08 1 129222376<br>    NbV1Ch08 AUGUSTUS        gene    7015    29794   0.01    -       .       ID=ACTG000000<br>    NbV1Ch08   AUGUSTUS        mRNA    7015    29794   0.01    -       .       ID=ACTG000000.t1;Parent=g1,ACTG000000<br>    NbV1Ch08   AUGUSTUS        transcription_end_site  7015    7015    .       -       .       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        three_prime_utr 7015    8531    0.2     -       .       ID=g1.t1.3UTR1;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        exon    7015    8747    .       -       .       ID=g1.t1.exon1;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        stop_codon      8532    8534    .       -       0       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        CDS     8532    8747    0.31    -       0       ID=g1.t1.CDS1;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08        AUGUSTUS        intron  8748    9191    0.49    -       .       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        CDS     9192    9342    0.66    -       1       ID=g1.t1.CDS2;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08        AUGUSTUS        exon    9192    9342    .       -       .       ID=g1.t1.exon2;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        intron  9343    9915    0.58    -       .       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        CDS     9916    10006   0.71    -       2       ID=g1.t1.CDS3;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08        AUGUSTUS        exon    9916    10006   .       -       .       ID=g1.t1.exon3;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        intron  10007   10101   0.74    -       .       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        CDS     10102   10201   0.78    -       0       ID=g1.t1.CDS4;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08        AUGUSTUS        exon    10102   10201   .       -       .       ID=g1.t1.exon4;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        intron  10202   10712   0.8     -       .       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        CDS     10713   11107   0.11    -       2       ID=g1.t1.CDS5;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08        AUGUSTUS        exon    10713   11107   .       -       .       ID=g1.t1.exon5;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        intron  11108   11569   0.07    -       .       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        CDS     11570   12151   0.09    -       2       ID=g1.t1.CDS6;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08        AUGUSTUS        exon    11570   12151   .       -       .       ID=g1.t1.exon6;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        intron  12152   12588   0.34    -       .       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        CDS     12589   12717   0.39    -       2       ID=g1.t1.CDS7;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08        AUGUSTUS        exon    12589   12717   .       -       .       ID=g1.t1.exon7;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        intron  12718   12789   0.42    -       .       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        CDS     12790   13075   0.39    -       0       ID=g1.t1.CDS8;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08        AUGUSTUS        exon    12790   13075   .       -       .       ID=g1.t1.exon8;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        intron  13076   14832   0.51    -       .       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        CDS     14833   15009   0.39    -       0       ID=g1.t1.CDS9;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08        AUGUSTUS        exon    14833   15009   .       -       .       ID=g1.t1.exon9;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        intron  15010   15278   0.59    -       .       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        CDS     15279   15415   0.56    -       2       ID=g1.t1.CDS10;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        exon    15279   15415   .       -       .       ID=g1.t1.exon10;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        intron  15416   15487   0.58    -       .       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        CDS     15488   15612   0.96    -       1       ID=g1.t1.CDS11;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        exon    15488   15612   .       -       .       ID=g1.t1.exon11;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        intron  15613   15706   0.96    -       .       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        CDS     15707   15957   0.98    -       0       ID=g1.t1.CDS12;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        exon    15707   15958   .       -       .       ID=g1.t1.exon12;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        start_codon     15955   15957   .       -       0       Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        five_prime_utr  15958   15958   0.99    -       .       ID=g1.t1.5UTR1;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        five_prime_utr  27458   28250   0.37    -       .       ID=g1.t1.5UTR2;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        exon    27458   28250   .       -       .       ID=g1.t1.exon13;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        five_prime_utr  29272   29794   0.08    -       .       ID=g1.t1.5UTR3;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08       AUGUSTUS        exon    29272   29794   .       -       .       ID=g1.t1.exon14;Parent=g1.t1,ACTG000000.t1<br>    NbV1Ch08      AUGUSTUS        transcription_start_site        29794   29794   .       -       .       Parent=g1.t1,ACTG000000.t1<br></i><br>Thank you in advance<br></div></div>