[Bioperl-l] Graphics:Panel /SeqFeature::Generic
Lincoln Stein
lstein at cshl.edu
Tue Dec 2 17:21:19 EST 2003
Make sure to set the tag on the subfeatures and to use the segments glyph.
The attached demo script encodes the score as red/blue and the significance
as height.
Lincoln
On Monday 24 November 2003 07:25 am, Daniel Lang wrote:
> Hi Lincoln,
> Thanks for your help, but this didn´t improve the situation:(
> I know now for sure, that the $feature->score is not the evalue, that is
> set in the while loop, but the normal score!!
> Additionally, I tried again introducing it as an additional tag, but
> this tag isn´t available in the callback with e.g.
> get_tag_values('evalue'). I´m using it in a mod_perl Handler, could this be
> part of the problem? Thanks in advance,
> Daniel
>
> Lincoln Stein wrote:
> > Hi Dan,
> >
> > Try changing the "generic" glyph to "segments." The first glyph doesn't
> > know how to deal with subparts (such as HSPs), the second does.
> >
> > Lincoln
> >
> > On Monday 17 November 2003 05:06 am, Daniel Lang wrote:
> >>Hi,
> >>I want to generate overview graphics from BLAST reports, where the hits
> >>are sorted and colored (>1e-10 -->green, ...)according their evalues...
> >>
> >>So I thought, I could solve this using a callback function for the
> >>bgcolor and using the 'low_score' sort_order, but when applied to a
> >>BLAST report, it results in sorted but only red hits?
> >>I also tried introducing the evalues as additional tags like done with
> >>'bits' or 'range', but when testing for this tag in the callback
> >>(has_tag) its not available?
> >>So I wander if the function is envoked for each hit in the while loop?
> >>
> >>Here the code sniplet:
> >>
> >>my $track = $panel->add_track(-glyph => 'generic',
> >> -label => 1,
> >> -connector => 'dashed',
> >> -height => 5,
> >> -bgcolor => sub {
> >> my $feature = shift;
> >> my $evalue = $feature->score;
> >> if ($evalue < 1e-10) {return 'green';}
> >> else {return 'red';}}
> >> ,
> >> -fontcolor => 'green',
> >> -font2color => 'red',
> >> -sort_order => 'low_score',
> >> -min_score => '1e-1000',
> >> -max_score => '10000',
> >> -description => sub {
> >> my $feature = shift;
> >> return unless
> >> $feature->has_tag('bits'); my ($description) =
> >>$feature->each_tag_value('bits');
> >> my $score = $feature->score;
> >> my ($range) =
> >>$feature->each_tag_value('range');
> >> "Score=$description bits, E-value=$score, $range";
> >> });
> >>
> >> while( my $hit = $result->next_hit ) {
> >> my $evalue = $hit->significance;
> >> my $feature = Bio::SeqFeature::Generic->new(-score => $evalue,
> >> -display_name => $hit->name,
> >> -tag => { 'bits' => $hit->bits,
> >> 'range' => "from ". $hit->start('query') . " to " .
> >>$hit->end('query'),
> >> },
> >> );
> >> while( my $hsp = $hit->next_hsp ) {
> >> $feature->add_sub_SeqFeature($hsp,'EXPAND');
> >> }
> >> $track->add_feature($feature);
> >> }
> >>
> >>Thanks in advance,
> >>Daniel
> >>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l at portal.open-bio.org
> >>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
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--
========================================================================
Lincoln D. Stein Cold Spring Harbor Laboratory
lstein at cshl.org Cold Spring Harbor, NY
========================================================================
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full_length:
hit:
description Human non-histone chromatin protein HMG1 (HMG1) gene, complete cds.
name U51677
hit:
description Mus musculus (clone Clebp-1) high mobility group 1 protein (HMG-1)
name L38477
hit:
description M.musculus HMG1 gene
name X80457
hit:
description Mus musculus HMG-1 mRNA, complete cds.
name U00431
hit:
description Human non-histone chromosomal protein (HMG-1) retropseudogene.
name L08048
hit:
description Human mRNA for high mobility group-1 protein (HMG-1).
name X12597
hit:
description Rat amphoterin mRNA, complete cds.
name M64986
hit:
description M.musculus mRNA for non-histone chromosomal high-mobility group 1
name Z11997
hit:
description Human mRNA for HMG-1, complete cds.
name D63874
hit:
description Human DNA sequence from BAC 445C9 on chromosome 22q12.1.
name Z95115
hit:
description Bovine mRNA for high mobility group 1 (HMG1) protein
name X12796
hit:
description Bovine high-mobility-group protein (HMG-1) mRNA, 3' end.
name M26110
hit:
description Mus musculus HMG-like protein (Trf) mRNA, complete cds.
name AF009343
hit:
description Pig nonhistone protein HMG1 mRNA, complete cds.
name M21683;M21684
hit:
description Homo sapiens (clone 06) high mobility group 1 protein mRNA
name L13805
hit:
description Human chromosomal protein HMG1 related gene.
name D14718
hit:
description Chinese hamster HMG-1 gene for high mobility group protein 1
name Y00365
hit:
description Rat high mobility group 1 protein synthetic gene, complete cds.
name M63852
hit:
description Rat mRNA for high mobility group protein HMG1
name Y00463
hit:
description M.musculus HMG1-R-227 gene
name X80466
hit:
description M.musculus HMG1-R-154 gene
name X80462
hit:
description M.musculus HMG1-R-145 gene
name X80461
hit:
description M.musculus HMG1-R-177 gene
name X80459
hit:
description M.musculus HMG1-R-87 gene
name X80467
hit:
description M.musculus HMG1-R-168 gene
name X80465
hit:
description M.musculus HMG1-R-159 gene
name X80463
hit:
description Rainbow trout HMG-1 gene exons 2-5, complete cds.
name L32859
hit:
description M.musculus HMG1-R-135 gene
name X80460
hit:
description M.musculus HMG1-R-161 gene
name X80464
hit:
description Trout mRNA for high mobility group protein HMG-T
name X02666
hit:
description Xenopus laevis high mobility group protein-1 (HMG-1) mRNA, complete
name U21933
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