[Gmod-help] Re: [Gmod-gbrowse] Problems with Bio::DB::SeqFeature::Store and gff3
Jason Stajich
jason at bioperl.org
Thu Sep 11 22:47:19 EDT 2008
Your chromosome feature isn't GFF3.
OAR1 . chromosome 1 80000 . + . Sequence OAR
Should probably be
OAR1 . chromosome 1 80000 . + . ID=OAR;Name=OAR
Not sure this solves the problem of course.
You may eventually need to covert to 3-level GFF3 where you have
gene,mRNA, and CDS/exon.
You are welcome to try my data which has been working fine for me.
http://fungalgenomes.org/data/GFF/
like
http://fungalgenomes.org/data/GFF/Yarrowia_lipolytica_CLIB122.07-APR-2006.gff3.gz
Just grab the first 10-20 lines of it, it has chromosome info in it as
well.
-jason
On Sep 11, 2008, at 7:10 PM, Smithies, Russell wrote:
> I've spent all morning trying to get gff3 data to display after
> loading into a SeqFeature database and I'm getting nowhere :-(
> We installed the fresh GBrowse 1.69 release yesterday and had to
> upgrade to bioperl-live as the version of Bioperl we were using
> (also the latest release) was too low according to the install script.
>
> Our old GBrowse instances using gff2 data and MySQL are still
> running fine so I assume it's not BioPerl that's broken.
> But when I try to search for anything on our new gff3 GBrowse, I get
> the usual "landmark maned foobar is not recognized" on the webpage.
> The error logs are full of this rather cryptic message:
> -------------------------------------------------
> [Fri Sep 12 13:59:38 2008] [error] [client 147.158.129.160]
> Bio::Graphics::BrowserConfig=HASH(0x1742be30) at /usr/lib64/perl5/
> site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> line 587., referer: http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1
> [Fri Sep 12 13:59:38 2008] [error] [client 147.158.129.160]
> Bio::Graphics::BrowserConfig=HASH(0x1742be30) at /usr/lib64/perl5/
> site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> line 587., referer: http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1
> [Fri Sep 12 13:59:38 2008] [error] [client 147.158.129.160]
> Bio::Graphics::BrowserConfig=HASH(0x1742be30) at /usr/lib64/perl5/
> site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> line 587., referer: http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1
> [Fri Sep 12 13:59:38 2008] [error] [client 147.158.129.160]
> Bio::Graphics::BrowserConfig=HASH(0x1742be30) at /usr/lib64/perl5/
> site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> line 587., referer: http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1
> [Fri Sep 12 13:59:38 2008] [error] [client 147.158.129.160] Use of
> uninitialized value in split at /var/www/gbrowse/cgi-bin/gbrowse
> line 1682., referer: http://devgbrowse.agresearch.co.nz/cgi-bin/gbrowse/dev_oar/?reset=1
> -------------------------------------------------
>
> I've kept my config to a minimum to try and debug:
>
> -------------------------------------------------
> [GENERAL]
> description = DEVELOPMENT OAR true chromosomes
>
> db_adaptor = Bio::DB::SeqFeature::Store
> db_args = -adaptor DBI::mysql
> -dsn
> dbi:mysql:database=dev_oar_chromosomes;host=gbrowsemysql
> user = username
> pass = password
>
> initial landmark = OAR1:76900..77100
>
> # examples to show in the introduction
> examples = OAR1:100..500 XM_001256510 XM_001250379
>
> # Web site configuration info
> stylesheet = /gbrowse/gbrowse.css
> buttons = /gbrowse/images/buttons
> tmpimages = /gbrowse/tmp
>
> [TRACK DEFAULTS]
> glyph = generic
> height = 8
> fgcolor = black
> font2color = gray
> label density = 800
> bump density = 10000
> link_target = _blank
>
>
> [Test]
> feature = mRNA
> glyph = cds
> description = 1
> key = Test
> citation = test
> ------------------------------------------------------------------------------
>
> And the gff3 data looks like this:
>
>
> ------------------------------------------------------------------------------
> ##gff-version 3
> OAR1 . chromosome 1 80000 . + . Sequence OAR1
> OAR1 btref mRNA 2988 20491 3756 + .
> ID=XM_001256510;Target=XM_001256510+1+2278;Note=PREDICTED:+Bos+taurus
> +hypothetical+protein+LOC767882+(LOC767882)%2C+partial
> +mRNA;Entrez_Gene=767882;GO=GO:0003723;GO_Term=RNA+binding
> OAR1 btref exon 2988 3049 3756 + .
> Parent=XM_001256510;Target=XM_001256510+1+62
> OAR1 btref exon 4092 4204 3756 + .
> Parent=XM_001256510;Target=XM_001256510+63+175
> OAR1 btref exon 6060 6219 3756 + .
> Parent=XM_001256510;Target=XM_001256510+176+335
> OAR1 btref exon 7066 7175 3756 + .
> Parent=XM_001256510;Target=XM_001256510+440+549
> OAR1 btref exon 11913 12119 3756 + .
> Parent=XM_001256510;Target=XM_001256510+550+756
> OAR1 btref exon 12367 12582 3756 + .
> Parent=XM_001256510;Target=XM_001256510+757+972
> OAR1 btref exon 13003 13209 3756 + .
> Parent=XM_001256510;Target=XM_001256510+973+1179
> OAR1 btref exon 13333 13440 3756 + .
> Parent=XM_001256510;Target=XM_001256510+1180+1287
> OAR1 btref exon 14246 14350 3756 + .
> Parent=XM_001256510;Target=XM_001256510+1288+1392
> OAR1 btref exon 14626 14704 3756 + .
> Parent=XM_001256510;Target=XM_001256510+1393+1471
> OAR1 btref exon 15944 16084 3756 + .
> Parent=XM_001256510;Target=XM_001256510+1472+1612
> OAR1 btref exon 16735 16748 3756 + .
> Parent=XM_001256510;Target=XM_001256510+1618+1631
> OAR1 btref exon 16751 16834 3756 + .
> Parent=XM_001256510;Target=XM_001256510+1633+1716
> OAR1 btref exon 16956 17069 3756 + .
> Parent=XM_001256510;Target=XM_001256510+1717+1830
> OAR1 btref exon 17844 17930 3756 + .
> Parent=XM_001256510;Target=XM_001256510+1831+1917
> OAR1 btref exon 20262 20491 3756 + .
> Parent=XM_001256510;Target=XM_001256510+2049+2278
> OAR1 btref mRNA 76974 77060 174 - .
> ID=XM_001250379;Target=XM_001250379+10+100;Note=PREDICTED:+Bos+taurus
> +similar+to+FARP2+protein+(LOC781869)%2C+mRNA;Entrez_Gene=781869
> OAR1 btref exon 76974 76977 174 - .
> Parent=XM_001250379;Target=XM_001250379+97+100
> OAR1 btref exon 76978 77053 174 - .
> Parent=XM_001250379;Target=XM_001250379+20+95
> OAR1 btref exon 77054 77060 174 - .
> Parent=XM_001250379;Target=XM_001250379+10+16
> ---------------------------------------------------------------------------
>
>
> As far as I can see, the database is loading correctly:
>
> ----------------------------------------------
> [smithiesr at impala oar]$ bp_seqfeature_load.pl --create --verbose --
> fast --user username --password password -dsn
> 'dbi:mysql:host=gbrowsemysql;database=dev_oar_chromosomes' dev_gff/
> OAR1.test.gff3
> loading dev_gff/OAR1.test.gff3...
>
> Building object tree... 0.00s
> Loading bulk data into database... 0.01s
> load time: 0.07s
> ------------------------------------------------
>
> Any ideas what to try next??
> Have I overlooked something obvious?
>
>
> Thanx,
>
>
> Russell Smithies
>
> Bioinformatics Applications Developer
> Invermay Research Centre
> Puddle Alley,
> Mosgiel,
> New Zealand
> www.agresearch.co.nz
>
>
>
>
>
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Jason Stajich
jason at bioperl.org
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