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Re: [Gmod-ajax] generate-names.pl does not have any effect
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From: Colin <col...@gm...> - 2019-08-12 15:08:19
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Hi there, The main thing to note is that generate-names.pl does not accept a specific file as input. By default, generate-names.pl runs on the whole data data directory that you provide to the --out parameter, so you just use bin/generate-names.pl --out /efs/apollo/Nitab-v4.5 This automatically detects the tracks you have loaded in this directory and populates the "names" folder. You can use the -v argument to get verbose. The --tracks argument can accept a list of comma separated track "labels" from the trackList.json/tracks.conf -Colin On Mon, Aug 12, 2019 at 8:39 AM Michał T. Lorenc <m.t...@gm...> wrote: > Hi Scott, > I think, I ran *flatfile-to-json.pl <http://flatfile-to-json.pl>* first > and it generated the following folders: > > > > > > > > > > > > */efs/apollo/Nitab-v4.5$ ls -hlattotal 4.1Gdrwxr-sr-x 10 ubuntu > apollo_users 6.0K Aug 12 04:16 ..-rw-rw-r-- 1 ubuntu apollo_users 541 Aug > 11 23:33 .htaccessdrwxrwsr-x 2 ubuntu apollo_users 14K Aug 11 23:05 > names-rw-rw-r-- 1 ubuntu apollo_users 819 Aug 11 23:04 > trackList.jsondrwxrwsr-x 4 ubuntu apollo_users 6.0K Jul 14 22:23 > tracks-rw-rw-r-- 1 ubuntu apollo_users 0 Jul 14 12:21 > tracks.confdrwxrwsr-x 26 ubuntu apollo_users 6.0K Jul 14 12:21 > seq-rw-rw-r-- 1 ubuntu apollo_users 49M Jul 14 02:39 > Nitab-v4.5_gene_models_Chr_Edwards2017.gff-rw-rw-r-- 1 ubuntu apollo_users > 2.8G Jul 14 02:24 Nitab-v4.5_genome_Chr_Edwards2017.fasta* > > What did I miss? > > Thank you in advance, > > Michal > > On Mon, Aug 12, 2019 at 2:57 PM Scott Cain <sc...@sc...> wrote: > >> Hi Michal, >> >> Did you run flatfile-to-json.pl first? It creates a set of names.txt >> files that are required for generate-names to work on. >> >> Scott >> >> >> On Aug 11, 2019, at 7:20 PM, Michał T. Lorenc <m.t...@gm...> >> wrote: >> >> Hi all, >> I tried to use `generate-names.pl` in the following way: >> >> ``` >> >> *> /efs/apollo/Nitab-v4.5$ perl >> ~/tomcat7-deploy/apollo/jbrowse/bin/prepare-refseqs.pl >> <http://prepare-refseqs.pl> --fasta >> /efs/apollo/Nitab-v4.5_genome_Chr_Edwards2017.fasta --out >> /efs/apollo/Nitab-v4.5> /efs/apollo/Nitab-v4.5$ perl >> ~/tomcat7-deploy/apollo/jbrowse/bin/generate-names.pl >> <http://generate-names.pl> --tracks >> Nitab-v4.5_gene_models_Chr_Edwards2017.gff --out /efs/apollo/Nitab-v4.5* >> ``` >> on the below GFF3 file: >> ``` >> >> >> >> >> >> >> >> >> >> *> cat Nitab-v4.5_gene_models_Chr_Edwards2017.gff...Nt01 maker gene >> 513567 517023 . - . >> ID=Nitab4.5_0002367g0080;Name=Nitab4.5_0002367g0080;Parent=Nitab4.5_0002367Nt01 >> maker mRNA 513567 517023 . - . >> ID=Nitab4.5_0002367g0080.1;Parent=Nitab4.5_0002367g0080;Name=Nitab4.5_0002367g0080.1;_AED=0.01;_eAED=0.01;_QI=61|1|1|1|1|1|2|173|194;Note="Ribosomal >> protein S6%2C plastid/chloroplast%2C Translation elongation factor >> EF1B/ribosomal protein S6%2C Ribosomal protein S6"Nt01 maker exon >> 513567 513979 . - . >> ID=Nitab4.5_0002367g0080.1:exon:2876;Parent=Nitab4.5_0002367g0080.1Nt01 >> maker exon 516618 517023 . - . >> ID=Nitab4.5_0002367g0080.1:exon:2875;Parent=Nitab4.5_0002367g0080.1Nt01 >> maker five_prime_UTR 516963 517023 . - . >> ID=Nitab4.5_0002367g0080.1:five_prime_utr;Parent=Nitab4.5_0002367g0080.1Nt01 >> maker CDS 516618 516962 . - 0 >> ID=Nitab4.5_0002367g0080.1:cds;Parent=Nitab4.5_0002367g0080.1Nt01 maker >> CDS 513740 513979 . - 0 >> ID=Nitab4.5_0002367g0080.1:cds;Parent=Nitab4.5_0002367g0080.1Nt01 maker >> three_prime_UTR 513567 513739 . - . >> ID=Nitab4.5_0002367g0080.1:three_prime_utr;Parent=Nitab4.5_0002367g0080.1* >> ``` >> >> Unfortunately, it did not work. What did I miss? >> >> Thank you in advance. >> >> Michal >> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> >> _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
