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Re: [Gmod-ajax] Loading GFF trouble
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From: Shankar A. S. <sha...@gm...> - 2009-10-19 14:11:15
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Hi Martin, I've had similar issues when using flatfile-to-json.pl. I have since switched to using biodb-to-json.pl with a conf file to load features. If you add "Name=" key value pairs to your feature attributes, these will be displayed as labels under your feature (see demo). You will also find that the full chromosome-length feature, and 7 seven others, disappear when you use biodb-to-json.pl Shankar On Mon, Oct 19, 2009 at 7:52 AM, Martin A. Hansen <ma...@ma...> wrote: > Right, that did the trick. > > But clicking on a feature shows ID undefined? and strand is shown as either > 1 or -1. > > Also, I have a feature that is full chromosome length (2.8M) and 7 that are > 0.5M. Strange? > > > > > Martin > > On Mon, Oct 19, 2009 at 1:27 PM, Colin Davenport <col...@ho...> > wrote: >> >> Hi Martin, >> >> I had a similar problem. >> >> I think this should help : you need to modify the GFF header >> and add a line >> >> ##sequence-region scf1117875581239 1 719819 >> >> Source was this tutorial >> >> http://gmod.org/wiki/JBrowse_Tutorial#Moving_work_to_the_client >> >> Hope that helps >> >> Colin >> >> >> >> >> >> ________________________________ >> Date: Mon, 19 Oct 2009 12:33:24 +0200 >> From: ma...@ma... >> To: gmo...@li... >> Subject: [Gmod-ajax] Loading GFF trouble >> >> Hello, >> >> >> I am trying to visualize some Bowtie hits of small sequences mapped to a >> bacterial genome. >> >> I have Apache and Jbrowse up and running. >> >> I have loaded the genome sequence using prepare-refseqs.pl from the www >> root - and it is visible in Jbrowse. >> >> Now, loading some GFF3 data gives trouble: >> >> bin/flatfile-to-json.pl -gff /Users/maasha/DATA/Assembly/foo.gff >> --tracklabel test1 --key 'human readable test' >> >> working on seq S.aur_COL >> Didn't find a segment with name S.aur_COL >> Use of uninitialized value in string eq at bin/flatfile-to-json.pl line >> 178, <GEN2> line 24. >> >> >> The GFF data looks like this (may be malformatted?): >> >> ##gff-version 3 >> S.aur_COL BOWTIE . 2474533 2474567 1 + . >> ID=5_BWCOjxwXsN1/1 >> S.aur_COL BOWTIE . 1980530 1980564 3 + . >> ID=7_NZCOjxwXsN1/1 >> S.aur_COL BOWTIE . 2115669 2115703 3 + . >> ID=7_NZCOjxwXsN1/1 >> S.aur_COL BOWTIE . 2232159 2232193 3 + . >> ID=7_NZCOjxwXsN1/1 >> S.aur_COL BOWTIE . 530658 530692 3 - . >> ID=7_NZCOjxwXsN1/1 >> S.aur_COL BOWTIE . 574288 574322 3 - . >> ID=7_NZCOjxwXsN1/1 >> S.aur_COL BOWTIE . 579500 579534 3 - . >> ID=7_NZCOjxwXsN1/1 >> S.aur_COL BOWTIE . 2721172 2721206 1 + . >> ID=3_2VCOjxwXsN1/1 >> S.aur_COL BOWTIE . 575753 575787 3 + . >> ID=1_GbCOjxwXsN1/1 >> >> >> refseq.js looks like this: >> >> >> refSeqs = >> [ >> { >> "length" : 2809422, >> "name" : "S.aur_COL", >> "seqDir" : "data/seq/S.aur_COL", >> "start" : 0, >> "end" : 2809422, >> "seqChunkSize" : 20000 >> } >> ] >> >> I cannot tell what version or revision my Jbrowse installation is (how do >> I find out?). >> >> So what is this segment error? And how do I resolve it? >> >> >> >> Cheers, >> >> >> >> Martin >> >> >> ________________________________ >> So gehst du mir nicht vor die Tür! Herbsttrends entdecken > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > |
