Menu
▾
▴
gmod-ajax
|
From: Martin A. H. <ma...@ma...> - 2009-10-19 10:33:40
|
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
|
|
From: Colin D. <col...@ho...> - 2009-10-19 11:27:37
|
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_COLDidn'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 3S.aur_COL BOWTIE . 2474533 2474567 1 + . ID=5_BWCOjxwXsN1/1 S.aur_COL BOWTIE . 1980530 1980564 3 + . ID=7_NZCOjxwXsN1/1S.aur_COL BOWTIE . 2115669 2115703 3 + . ID=7_NZCOjxwXsN1/1 S.aur_COL BOWTIE . 2232159 2232193 3 + . ID=7_NZCOjxwXsN1/1S.aur_COL BOWTIE . 530658 530692 3 - . ID=7_NZCOjxwXsN1/1 S.aur_COL BOWTIE . 574288 574322 3 - . ID=7_NZCOjxwXsN1/1S.aur_COL BOWTIE . 579500 579534 3 - . ID=7_NZCOjxwXsN1/1 S.aur_COL BOWTIE . 2721172 2721206 1 + . ID=3_2VCOjxwXsN1/1S.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 _________________________________________________________________ http://redirect.gimas.net/?n=M0910xHerbstmode2_WW So gehst du mir nicht vor die Tür! Herbsttrends entdecken |
|
From: Martin A. H. <ma...@ma...> - 2009-10-19 11:52:31
|
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<http://redirect.gimas.net/?n=M0910Herbstmode_WW> > |
|
From: Shankar A. S. <sha...@gm...> - 2009-10-19 14:11:15
|
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 > > |
|
From: Mitch S. <mit...@be...> - 2009-10-21 03:23:39
|
Martin A. Hansen wrote:
> But clicking on a feature shows ID undefined? and strand is shown as
> either 1 or -1.
The ID thing was kind of a mis-labeling; JBrowse can optionally keep
track of a separate "name" and "ID", but sometimes identifiers become
names and vice versa. I clarified the click-popup to show name and ID
separately, and modified flatfile-to-json.pl to include the ID from the
GFF as the ID in JBrowse, rather than the autogenerated one that
Bio::DB::SeqFeature::Store creates.
> Also, I have a feature that is full chromosome length (2.8M) and 7
> that are 0.5M. Strange?
The full length feature is from the sequence-region header; now that you
don't need that anymore, you can leave it out. Alternatively, you can
use the --type command line option to filter out the full length feature.
The long features are probably due to the fact that you have several
features with the same ID. I believe the bioperl code is merging them
together.
Mitch
>
>
>
> ##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
> <http://redirect.gimas.net/?n=M0910Herbstmode_WW>
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> 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
>
|
|
From: Mitch S. <mit...@be...> - 2009-10-21 03:17:14
|
Colin Davenport wrote: > I think this should help : you need to modify the GFF header > and add a line > ##sequence-region scf1117875581239 1 719819 > Thanks for answering this question, Colin. It seems like this bites a lot of people; I thought it had to be that way because of the chado adapter. But I found out a little while ago from Scott that he implemented some functionality in the chado adapter so that I could re-write the JBrowse code to drop this requirement. So, as of now, you no longer need a sequence-region header in your GFF. Mitch |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X