Bio::SeqFeature::Generic add_track duplicate labels
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Bio::SeqFeature::Generic add_track duplicate labels
by Mark Lewis-6
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Hello, I've been looking for quite some time into a why I'm getting duplicate labels on sequence features I'm creating with the loop below. An image of the output is here: http://interspersedata.com/pure/pureOTRACK-30449039-CRSPLOT-9973-1.png The loop: for ($i = 1; $i <= $numImg; $i++) { ## make a panel to store all the glyphs in this row. multiple glyphs occur is they collide due to ## the use of the bump feature. # $panel = Bio::Graphics::Panel->new(-length => $zoom, # length of panel in nucleotides -width => $imgWidth, # physical width of img in px -pad_top => 10, # padding -pad_bottom => 10, -pad_left => 10, -pad_right => 10, -bgcolor => $bgColour, # colors -grid => 'true', -gridcolor => '#cccccc', -gridmajorcolor => '#888888', -all_callbacks => 'true', # for coloured URE bars -key_font => 'gdTinyFont', -offset => $offset, # decremented by $zoom at loop end ); ## create current scale # $end = $offset + $zoom; if ($end >= 0) { # we've gone past the end, so we go *to* the end of the rope $end = -1; $numImg = 0; # this iteration will proceed, but the next redundant one won't } ## create new generic sequence feature and attach dna # $segment = Bio::SeqFeature::Generic->new(-start=>$offset,-end=>$end); $panel->add_track($segment, -glyph => 'anchored_arrow', -tick => 2, -fontcolor => '#333333', # reference track font colour -fgcolor => '#333333', # reference track colour -bgcolor => $bgColour ); ## define glyph track - this contains the glyphs (UREs) - you can have >1 tracks # # # # # # # # # # # # # my($track) = $panel->add_track( -glyph => 'segments', -linewidth => 2, -height => 8, -fontcolor => $txtCol, -label => 1, -description => 1, -bgcolor => sub { my($feat) = shift; my($score) = $feat->score; return ($cols[$score]); }, -bump => 1 ); ## get the data from hash and add it ## tabulated results with alternating coloured rows # foreach $ure (sort(keys %{$results{$rec}{$str}{ures}})) { foreach $instance (sort(keys %{$results{$rec}{$str}{ures}{$ure}})) { #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#= ## start loc = end location = length = name of URE = sequence of URE = category of URE = colour # # if ($results{$rec}{$str}{'ures'}{$ure}{$instance} =~ /^(-\d+)=(-\d+)=(\d+)=(.+?)=(.+?)=(.+?)=(.+?)$/) { $SEQlen = $3; $SEQname = $4; $SEQstart = $1; $SEQseq = $5; $trueEnd = $2; $SEQend = $2 - 1; # -1 as only 5 segments between start and end #$SEQcat = $6; $SEQcol = $colours{$7}; # get number from the colours hash } if ($SEQstart <= ($offset - ($SEQlen - 1)) || $SEQstart > $end) { # only deal with UREs in range next; } ## if the sequence is unnamed, use the sequence in the image, its more help # if ($SEQname eq "unnamed") { $SEQname = $SEQseq; } my($featureId) = "Name: $SEQname<br />Sequence: $SEQseq<br />Location: $SEQstart → $trueEnd"; my($feature) = Bio::SeqFeature::Generic->new(-display_name => $SEQname, -score => $SEQcol, -start => $SEQstart, -end => $SEQend, -tag => { new => 1, id => $featureId } ); $track->add_feature($feature); ## THIS ADDS A FEATURE WITH DOUBLE-THE-LABELS } ## end foreach $instance (sort(keys... } ## end foreach $ure (keys %ureLocs) I've been racking my brains for a long time and haven't found a solution. If I remove the label, both labels are removed. I'd be over the moon if someone could at least comment on where they think I might be going wrong or where I can look. I've read the CPAN docs several times and cannot see anything new to try. Many thanks IA Mark -- mq mindrail.net ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Bio::SeqFeature::Generic add_track duplicate labels
by Scott Cain-4
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Hi Mark,
This is really a Bio::Graphics question and should probably be asked on the bioperl mailing list. I've seen similar things when I was developing the Chado adaptor for GBrowse, but I don't remember what I did to cause it or how I fixed it. When you ask on the bioperl mailing list, pleas include sample data that can reproduce the behavior. Scott On Oct 29, 2009, at 10:21 PM, mark lewis wrote: > > Hello, > > I've been looking for quite some time into a why I'm getting duplicate > labels on sequence features I'm creating with the loop below. An > image of > the output is here: > > http://interspersedata.com/pure/pureOTRACK-30449039-CRSPLOT-9973-1.png > > > The loop: > > for ($i = 1; $i <= $numImg; $i++) { > ## make a panel to store all the glyphs in this row. multiple > glyphs occur > is they collide due to > ## the use of the bump feature. > # > $panel = Bio::Graphics::Panel->new(-length => $zoom, > # length of panel in nucleotides > -width => $imgWidth, # physical width of img > in px > -pad_top => 10, # padding > -pad_bottom => 10, > -pad_left => 10, > -pad_right => 10, > -bgcolor => $bgColour, # colors > -grid => 'true', > -gridcolor => '#cccccc', > -gridmajorcolor => '#888888', > -all_callbacks => 'true', # for coloured URE bars > -key_font => 'gdTinyFont', > -offset => $offset, > # decremented by $zoom at loop end > ); > > ## create current scale > # > $end = $offset + $zoom; > if ($end >= 0) { # we've gone past the > end, so we > go *to* the end of the rope > $end = -1; > $numImg = 0; # this iteration will > proceed, but > the next redundant one won't > } > > ## create new generic sequence feature and attach dna > # > $segment = Bio::SeqFeature::Generic->new(-start=>$offset,-end=>$end); > > $panel->add_track($segment, > -glyph => 'anchored_arrow', > -tick => 2, > -fontcolor => '#333333', # reference track font colour > -fgcolor => '#333333', # reference track colour > -bgcolor => $bgColour > ); > > ## define glyph track - this contains the glyphs (UREs) - you can > have >1 > tracks # # # # # # # # # # # # > # > my($track) = $panel->add_track( > -glyph => 'segments', > -linewidth => 2, > -height => 8, > -fontcolor => $txtCol, > -label => 1, > -description => 1, > -bgcolor => sub { > my($feat) = shift; > my($score) = $feat->score; > return ($cols[$score]); > }, > -bump => 1 > ); > > ## get the data from hash and add it > ## tabulated results with alternating coloured rows > # > foreach $ure (sort(keys %{$results{$rec}{$str}{ures}})) { > foreach $instance (sort(keys %{$results{$rec}{$str}{ures}{$ure}})) { > #= > #= > #= > #= > #= > #= > #= > #= > #= > #= > #= > #= > #= > #= > #= > #=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#=#= > ## start loc = end location = length = name of URE = sequence of URE = > category of URE = colour > # > # > if ($results{$rec}{$str}{'ures'}{$ure}{$instance} =~ > /^(-\d+)=(-\d+)=(\d+)=(.+?)=(.+?)=(.+?)=(.+?)$/) { > $SEQlen = $3; > $SEQname = $4; > $SEQstart = $1; > $SEQseq = $5; > $trueEnd = $2; > $SEQend = $2 - 1; # -1 as only 5 segments between start and end > #$SEQcat = $6; > $SEQcol = $colours{$7}; # get number from the colours hash > } > > if ($SEQstart <= ($offset - ($SEQlen - 1)) || $SEQstart > $end) > { # only > deal with UREs in range > next; > } > > ## if the sequence is unnamed, use the sequence in the image, its > more help > # > if ($SEQname eq "unnamed") { > $SEQname = $SEQseq; > } > > my($featureId) = "Name: $SEQname<br />Sequence: $SEQseq<br / > >Location: > $SEQstart → $trueEnd"; > my($feature) = > Bio::SeqFeature::Generic->new(-display_name => $SEQname, > -score => $SEQcol, > -start => $SEQstart, > -end => $SEQend, > -tag => { new => 1, > id => $featureId } > ); > $track->add_feature($feature); ## THIS ADDS A FEATURE WITH > DOUBLE-THE-LABELS > } ## end foreach $instance (sort(keys... > } ## end foreach $ure (keys %ureLocs) > > I've been racking my brains for a long time and haven't found a > solution. > If I remove the label, both labels are removed. I'd be over the > moon if > someone could at least comment on where they think I might be going > wrong > or where I can look. I've read the CPAN docs several times and > cannot see > anything new to try. > > Many thanks IA > Mark > -- > mq > mindrail.net > > ------------------------------------------------------------------------------ > 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-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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