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Re: [Gmod-ajax] changing ID in an existing GFF3 file
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From: Fields, C. J <cjf...@il...> - 2020-01-21 01:16:42
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I vaguely recall doing something like this a few years ago w/ Bio::FeatureIO but it was custom. Would this be possible in Bio::DB::SeqFeature?
chris
From: Scott Cain <sc...@sc...>
Date: Monday, January 20, 2020 at 6:52 PM
To: "Michał T. Lorenc" <m.t...@gm...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] changing ID in an existing GFF3 file
Hi Michal,
I don't know of any general purpose script for doing that. If I were writing one, I'd probably do it with a perl script that used Bio::FeatureIO::gff, but then, I'm old :-)
Sorry I couldn't be more helpful,
Scott
On Sun, Jan 19, 2020 at 1:59 PM Michał T. Lorenc <m.t...@gm...<mailto:m.t...@gm...>> wrote:
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,
Michal
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Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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