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Re: [Gmod-gbrowse] features not displaying
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From: Hilmar L. <hl...@gn...> - 2005-01-28 19:31:11
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So how do others do this then on biosql? Simon ran a benchmark that included biosql. Ah - that was on an artifical dataset, right? I thought Simon's been running gbrowse on top of biosql for some demo site on real data? So this may need more work then in that the bridging code should query either bioentry, or seqfeature, or possibly both, maybe configurable? -hilmar On Thursday, January 27, 2005, at 12:59 PM, Marc Logghe wrote: > Hi Genevieve, > my posts to gmo...@li... seem to get lost one > way or another. > > Anyhow, I am afraid I will not be able to help you out ... > I can only make a few remarks. > As far as I understand your pseudomonas biosql database contains 1 > bioentry with the accession NC_004578 and sequence length 6397126 bp. > A query in the gbrowse/biosql combination will only work for that > accession and will return the complete segment. So I guess you get a > kind of timeout because the the fetching of the bioentry from biosql > takes too long. > Also, as far as I know, it is not possible to query for features > residing on that segment, e.g. the gene PSPTO0041. That is because > gbrowse/biosql will only look for the bioentry in biosql with the > accession number PSPTO0041 and not the gene feature with that > locus_tag ! > This is probably not the behaviour you want. > An option I see, is that you convert the genbank record into gff and > load that in gbrowse/chado or gbrowse/gff. > I think genbank2gff3.pl is especially suited to do the conversion. > Hope I am not terribly wrong here ... > > Regards, > Marc > > >> -----Original Message----- >> From: Genevieve DeClerck [mailto:ga...@co...] >> Sent: Thursday, January 27, 2005 6:14 PM >> To: Marc Logghe >> Cc: gmo...@li... >> Subject: Re: [Gmod-gbrowse] features not displaying >> >> >> >> Right, thanks Marc - I lost that line when I created my conf >> file from >> scratch (from 06.biosql.conf) for the umpteenth time. With that line >> (and init_code.pl) I can successfully get the cds in the 'parkin' >> example biosql database to display! So I moved to the next step and >> created a new biosql db and loaded it with data that I'm more >> interested >> in.. the gbk file from ncbi of Pseudomonas syringae features >> (ftp://bio-mirror.net/biomirror/ncbigenomes/Bacteria/Pseudomon >> as_syringae/NC_004578.gbk). >> >> >> I seem to be encountering a similar problem as with the >> example parkin >> db previous to adding back that line - everything appears to be >> operating correctly in the browser, no errors in the web log, but no >> features appear for CDS's or anything else. Translation frames, GC >> content and sequence display fine. >> >> I'm starting to think that there's something amiss with how the >> NC_004578.gbk data is stored in the database... or something that >> biosql/gbrowse doesn't like about it. However, I do not see anything >> weird with the data when I browse through it in mysql. THe >> conf file i'm >> using for the NC_004578 db is pretty much the same as what I used for >> the parkin db.. just the appropriate changes in the db_args def. >> >> Any thoughts? >> >> Thanks, >> Genevieve >> >> >> Marc Logghe wrote: >> >>> Hi Genevieve, >>> I am pretty sure it will be fixed when you adjust your conf >> like I suggested earlier. >>> >>> init_code = do "$main::CONF_DIR/init_code.pl"; >>> >>> >>> and put init_code.pl in your gbrowse.conf directory. >>> >>> >>> *Bio::SeqFeature::Generic::attributes = >> \&Bio::SeqFeature::Generic::get_tag_values; >>> *Bio::SeqFeature::Generic::method = >> \&Bio::SeqFeature::Generic::primary_tag; >>> *Bio::SeqFeature::Generic::type = sub { >>> my $feat = shift; >>> my ($method) = $feat->primary_tag; >>> my ($source) = $feat->source_tag; >>> return $method; >>> }; >>> *Bio::SeqFeature::Generic::name = sub { >>> my $feat = shift; >>> my $name = eval {($feat->get_tag_values('name'))[0]}; >>> $name ||= eval {($feat->get_tag_values('label'))[0]}; >>> $name ||= eval {($feat->get_tag_values('db_xref'))[0]}; >>> # $name ||= 'unknown'; >>> print STDERR "name = $name\n"; >>> return $name; >>> } >>> >>> >>> I tested it by commenting out the init_code line in my conf >> and I have the same things happening as you mention: no >> features show up, no errors in the log. >>> >>> ML >>> >>> >>> >>> >>> >>> >>>> Hi, >>>> >>>> I can't for the life of me figure out why features/glyphs are not >>>> displaying in gbrowse. Everything else in the browser page is >>>> displaying >>>> fine - the header section, the footer, etc. A couple of >>>> things display >>>> ok in the feature window... GC Content, Translation fwd and rev >>>> (including DNA sequence when zoomed all the way down). But no real >>>> features, such as CDS, are displayed. The CDS track has a >>>> label, "CDS," >>>> but the rest is just plain empty, where I know there should >>>> be a feature. >>>> >>>> I have gbrowse 1.62 running with a biosql-mysql database >> loaded with >>>> bioperl-db example data file 'parkin.gb', which has one CDS. >>>> [I just got >>>> this setup working yesterday, thanks to help from this list >>>> and BioSQL-l >>>> - see posts from jan 25 2005: "gbrowse on top of biosql"]. >>>> There are no >>>> errors in the web error log or the mysql log. I triple >>>> checked that the >>>> parkin data is actually in the database and it is. >>>> >>>> ..I'm thinking there must be something wrong with my gbrowse >>>> conf file >>>> for this database.. in particular in the track section. But >>>> if that were >>>> the case, wouldn't I be seeing errors in my httpd error >> log? The conf >>>> file i have is almost an exact copy of a conf file that i've seen >>>> referred to in the docs: 06.biosql.conf. The track stanzas look >>>> reasonable, going from info in docs and tutorial. >>>> How do I debug the conf file?? >>>> Or should I be looking somewhere else? >>>> >>>> My biosql.conf file is pasted below. >>>> >>>> Any clues much appreciated. >>>> >>>> Thanks, >>>> Genevieve >>>> >>>> #************** biosql.conf ***************** >>>> >>>> [GENERAL] >>>> description = biosql >>>> db_adaptor = Bio::DB::Das::BioSQL >>>> db_args = driver mysql >>>> dbname biosql >>>> namespace genbank >>>> host localhost >>>> user nobody >>>> pass '' >>>> >>>> plugins = SequenceDumper FastaDumper RestrictionAnnotator >>>> >>>> # Web site configuration info >>>> stylesheet = /gbrowse/gbrowse.css >>>> buttons = /gbrowse/images/buttons >>>> tmpimages = /gbrowse/tmp >>>> >>>> # where to link to when user clicks in detaild view >>>> #link = >>>> http://localhost/perl/gbrowse?ref=$ref;start=$start;stop=$end >>>> link = AUTO >>>> >>>> # what image widths to offer >>>> image widths = 450 640 800 1024 >>>> >>>> # default width of detailed view (pixels) >>>> default width = 800 >>>> default features = CDS >>>> >>>> >>>> # max and default segment sizes for detailed view >>>> max segment = 500000 >>>> default segment = 50000 >>>> >>>> # zoom levels >>>> zoom levels = 100 200 1000 2000 5000 10000 20000 40000 >>>> 100000 200000 >>>> 500000 1000000 >>>> low res = 200000 >>>> >>>> # colors of the overview, detailed map and key >>>> overview bgcolor = wheat >>>> detailed bgcolor = white >>>> key bgcolor = beige >>>> >>>> footer = <hr> >>>> <table width="100%"> >>>> <TR> >>>> <TD align="LEFT" class="databody"> >>>> For the source code for this browser, see the <a >>>> href="http://www.gmod.org"> >>>> Generic Model Organism Database Project.</a> For other >>>> questions, send >>>> mail to <a href="mailto:ls...@cs...">ls...@cs...</a>. >>>> </TD> >>>> </TR> >>>> </table> >>>> <hr> >>>> <pre>$Id: 06.biosql.conf,v 1.1 2003/06/26 12:32:23 >>>> lstein Exp $</pre> >>>> >>>> # examples to show in the introduction >>>> examples = AB019558 >>>> >>>> # "automatic" classes to try when an unqualified identifier is given >>>> automatic classes = Accession >>>> >>>> [TRACK DEFAULTS] >>>> glyph = generic >>>> height = 8 >>>> bgcolor = cyan >>>> fgcolor = cyan >>>> fontcolor = black >>>> font2color = blue >>>> label density = 25 >>>> bump density = 100 >>>> description = 1 >>>> >>>> >>>> ############################################################## >>>> ################## >>>> # the remainder of the sections configure particular features to sho >>>> ############################################################## >>>> ################## >>>> >>>> [CDS] >>>> feature = CDS >>>> glyph = transcript2 >>>> #glyph = generic >>>> bgcolor = turquoise >>>> fgcolor = black >>>> height = 10 >>>> connector = solid >>>> key = CDS >>>> >>>> [REPEAT] >>>> feature = repeat_region >>>> glyph = generic >>>> bgcolor = red >>>> height = 10 >>>> description = 1 >>>> key = Repeat regions >>>> >>>> [TranslationF] >>>> glyph = translation >>>> global feature = 1 >>>> frame0 = cadetblue >>>> frame1 = blue >>>> frame2 = darkblue >>>> height = 20 >>>> fgcolor = purple >>>> strand = +1 >>>> translation = 3frame >>>> key = 3-frame translation (forward) >>>> >>>> [DNA/GC Content] >>>> glyph = dna >>>> global feature = 1 >>>> height = 40 >>>> do_gc = 1 >>>> fgcolor = red >>>> axis_color = blue >>>> >>>> [TranslationR] >>>> glyph = translation >>>> global feature = 1 >>>> frame0 = darkred >>>> frame1 = red >>>> frame2 = crimson >>>> height = 20 >>>> fgcolor = blue >>>> strand = -1 >>>> translation = 3frame >>>> key = 3-frame translation (reverse) >>>> >>>> #**************************************************** >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------- >>>> This SF.Net email is sponsored by: IntelliVIEW -- Interactive >>>> Reporting >>>> Tool for open source databases. Create drag-&-drop reports. >> Save time >>>> by over 75%! Publish reports on the web. Export to DOC, >> XLS, RTF, etc. >>>> Download a FREE copy at http://www.intelliview.com/go/osdn_nl >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>> >>> >>> >> >> > > > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting > Tool for open source databases. Create drag-&-drop reports. Save time > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- |