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Re: [Gmod-ajax] changing ID in an existing GFF3 file
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From: Scott C. <sc...@sc...> - 2020-01-21 17:54:11
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Probably but I feel like it would be more complicated. On Mon, Jan 20, 2020 at 5:16 PM Fields, Christopher J <cjf...@il...> wrote: > 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...> > 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 > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > > -- > > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
