Off topic:renaming ID in GFF3 file
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mictadlo ▴ 10
@mictadlo-10885
Last seen 4.2 years ago

Hi all, I ran BRAKER2 annotation pipeline and now I would like to change the ids from e.g. g65212 to AT1G01010.1, AT1G01020.1, AT1G01030.1.... Is there a script available to change IDs in an existing GFF3 file?

NbV1Ch01    TAIR10  gene    5928    8737    .       -       .       ID=AT1G01020;Note=protein_coding_gene;Name=AT1G01020
NbV1Ch01    TAIR10  mRNA    5928    8737    .       -       .       ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1
NbV1Ch01    TAIR10  protein 6915    8666    .       -       .       ID=AT1G01020.1-Protein;Name=AT1G01020.1;Derives_from=AT1G01020.1
NbV1Ch01    TAIR10  five_prime_UTR  8667    8737    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  CDS     8571    8666    .       -       0       Parent=AT1G01020.1
NbV1Ch01    TAIR10  exon    8571    8737    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  CDS     8417    8464    .       -       0       Parent=AT1G01020.1
NbV1Ch01    TAIR10  exon    8417    8464    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  CDS     8236    8325    .       -       0       Parent=AT1G01020.1
NbV1Ch01    TAIR10  exon    8236    8325    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  CDS     7942    7987    .       -       0       Parent=AT1G01020.1
NbV1Ch01    TAIR10  exon    7942    7987    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  CDS     7762    7835    .       -       2       Parent=AT1G01020.1
NbV1Ch01    TAIR10  exon    7762    7835    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  CDS     7564    7649    .       -       0       Parent=AT1G01020.1
NbV1Ch01    TAIR10  exon    7564    7649    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  CDS     7384    7450    .       -       1       Parent=AT1G01020.1
NbV1Ch01    TAIR10  exon    7384    7450    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  CDS     7157    7232    .       -       0       Parent=AT1G01020.1
NbV1Ch01    TAIR10  exon    7157    7232    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  CDS     6915    7069    .       -       2       Parent=AT1G01020.1
NbV1Ch01    TAIR10  three_prime_UTR 6437    6914    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  exon    6437    7069    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  three_prime_UTR 5928    6263    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  exon    5928    6263    .       -       .       Parent=AT1G01020.1
NbV1Ch01    TAIR10  mRNA    6790    8737    .       -       .       ID=AT1G01020.2;Parent=AT1G01020;Name=AT1G01020.2;Index=1
NbV1Ch01    TAIR10  protein 7315    8666    .       -       .       ID=AT1G01020.2-Protein;Name=AT1G01020.2;Derives_from=AT1G01020.2
NbV1Ch01    TAIR10  five_prime_UTR  8667    8737    .       -       .       Parent=AT1G01020.2
NbV1Ch01    TAIR10  CDS     8571    8666    .       -       0       Parent=AT1G01020.2
NbV1Ch01    TAIR10  exon    8571    8737    .       -       .       Parent=AT1G01020.2
NbV1Ch01    TAIR10  CDS     8417    8464    .       -       0       Parent=AT1G01020.2
NbV1Ch01    TAIR10  exon    8417    8464    .       -       .       Parent=AT1G01020.2
NbV1Ch01    TAIR10  CDS     8236    8325    .       -       0       Parent=AT1G01020.2
NbV1Ch01    TAIR10  exon    8236    8325    .       -       .       Parent=AT1G01020.2
NbV1Ch01    TAIR10  CDS     7942    7987    .       -       0       Parent=AT1G01020.2
NbV1Ch01    TAIR10  exon    7942    7987    .       -       .       Parent=AT1G01020.2
NbV1Ch01    TAIR10  CDS     7762    7835    .       -       2       Parent=AT1G01020.2
NbV1Ch01    TAIR10  exon    7762    7835    .       -       .       Parent=AT1G01020.2
NbV1Ch01    TAIR10  CDS     7564    7649    .       -       0       Parent=AT1G01020.2
NbV1Ch01    TAIR10  exon    7564    7649    .       -       .       Parent=AT1G01020.2
NbV1Ch01    TAIR10  CDS     7315    7450    .       -       1       Parent=AT1G01020.2
NbV1Ch01    TAIR10  three_prime_UTR 7157    7314    .       -       .       Parent=AT1G01020.2
NbV1Ch01    TAIR10  exon    7157    7450    .       -       .       Parent=AT1G01020.2
NbV1Ch01    TAIR10  three_prime_UTR 6790    7069    .       -       .       Parent=AT1G01020.2
NbV1Ch01    TAIR10  exon    6790    7069    .       -       .       Parent=AT1G01020.2

Thank you in advance,

gff3 annotation • 221 views
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