Bio::Graphics::Glyph::ideogram - The "ideogram" glyph

- NAME
- SYNOPSIS
- DESCRIPTION

- OPTIONS

- UCSC TO GFF CONVERSION SCRIPT
- BUGS
- SEE ALSO
- AUTHOR
- CONTRIBUTORS

# NAME

Bio::Graphics::Glyph::ideogram - The "ideogram" glyph

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# SYNOPSIS

      See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

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# DESCRIPTION

This glyph draws a section of a chromosome ideogram. It relies on certain data from the feature to determine which color should be used (stain) and whether the segment is a telomere or centromere or a regular cytoband. The centromeres and 'var'-marked bands are rendered with diagonal black-on-white patterns if the "-patterns" option is true, otherwise they are rendered in dark gray. This is to prevent a libgd2 crash on certain 64-bit platforms when rendering patterned images.

The cytobandband features would typically be formatted like this in GFF3:

     ...
     ChrX    UCSC    cytoband        136700001       139000000       .       .       .       Parent=ChrX;Name=Xq27.1;Alias=ChrXq27.1;stain=gpos75;
     ChrX    UCSC    cytoband        139000001       140700000       .       .       .       Parent=ChrX;Name=Xq27.2;Alias=ChrXq27.2;stain=gneg;
     ChrX    UCSC    cytoband        140700001       145800000       .       .       .       Parent=ChrX;Name=Xq27.3;Alias=ChrXq27.3;stain=gpos100;
     ChrX    UCSC    cytoband        145800001       153692391       .       .       .       Parent=ChrX;Name=Xq28;Alias=ChrXq28;stain=gneg;
     ChrY    UCSC    cytoband        1       1300000 .       .       .       Parent=ChrY;Name=Yp11.32;Alias=ChrYp11.32;stain=gneg;

     which in this case is a GFF-ized cytoband coordinate file from UCSC:

     http://hgdownload.cse.ucsc.edu/goldenPath/hg16/database/cytoBand.txt.gz

     and the corresponding GBrowse config options would be like this to
     create an ideogram overview track for the whole chromosome:

     The 'chromosome' feature below would aggregated from bands and centromere using the default
     chromosome aggregator

     [CYT:overview]
     feature       = chromosome
     glyph         = ideogram
     fgcolor       = black
     bgcolor       = gneg:white gpos25:silver gpos50:gray
                     gpos:gray  gpos75:darkgray gpos100:black acen:cen gvar:var
     arcradius     = 6
     height        = 25
     bump          = 0
     label         = 0

     A script to reformat UCSC annotations to  GFF3 format can be found at
     the end of this documentation.

## OPTIONS

The following options are standard among all Glyphs. See the Bio::Graphics::Glyph manpage for a full explanation.

      Option      Description                      Default
      ------      -----------                      -------

      -fgcolor      Foreground color               black

      -outlinecolor Synonym for -fgcolor

      -linewidth    Line width                     1

      -height       Height of glyph                10

      -font         Glyph font                     gdSmallFont

      -connector    Connector type                 0 (false)

      -connector_color
                    Connector color                black

      -label        Whether to draw a label        0 (false)

      -description  Whether to draw a description  0 (false)

The following options are specific to the ideogram glyph.

      Option      Description                      Default
      ------      -----------                      -------

      -bgcolor    Band coloring string             none

      -bgfallback Coloring to use when no bands    yellow
                     are present

-bgcolor is used to map each chromosome band's "stain" attribute into a color or pattern. It is a string that looks like this:

      gneg:white gpos25:silver gpos50:gray \
      gpos:gray  gpos75:darkgray gpos100:black acen:cen gvar:var

This is saying to use "white" for features whose stain attribute is "gneg", "silver" for those whose stain attribute is "gpos25", and so on. Several special values are recognized: "stalk" draws a narrower gray region and is usually used to indicate an acrocentric stalk. "var" creates a diagonal black-on-white pattern. "cen" draws a centromere.

If -bgcolor is just a color name, like "yellow", the glyph will ignore all bands and just draw a filled in chromosome.

If -bgfallback is set to a color name or value, then the glyph will fall back to the indicated background color if the chromosome contains no bands.

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# UCSC TO GFF CONVERSION SCRIPT

The following short script can be used to convert a UCSC cytoband annotation file into GFF format. If you have the lynx web-browser installed you can call it like this in order to download and convert the data in a single operation:

      fetchideogram.pl http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/cytoBand.txt.gz

Otherwise you will need to download the file first. Note the difference between this script and input data from previous versions of ideogram.pm: UCSC annotations are used in place of NCBI annotations.

#!/usr/bin/perl

use strict; my %stains; my %centros; my %chrom_ends;

foreach (@ARGV) { if (/^(ftp|http|https):/) { $_ = "lynx --dump $_ |gunzip -c|"; } elsif (/\.gz$/) { $_ = "gunzip -c $_ |"; } print STDERR "Processing $_\n"; }

print "##gff-version 3\n"; while(<>) { chomp; `my($chr,$start,$stop,$band,$stain)` = split /\t/; $start++; $chr = ucfirst($chr); `if(!(exists($chrom_ends{$chr}))` || $chrom_ends{$chr} < $stop) { $chrom_ends{$chr} = $stop; } my ($arm) = $band =~ /(p|q)\d+/; $stains{$stain} = 1; if ($stain eq 'acen') { $centros{$chr}->{$arm}->{start} = $stop; $centros{$chr}->{$arm}->{stop} = $start; next; } $chr =~ s/chr//i; print qq/$chr\tUCSC\tcytoband\t$start\t$stop\t.\t.\t.\tParent=$chr;Name=$chr;Alias=$chr$band;stain=$stain;\n/; }

foreach my $chr(sort keys %chrom_ends) { my $chr_orig = $chr; $chr =~ s/chr//i; print qq/$chr\tUCSC\tcentromere\t$centros{$chr_orig}->{p}->{stop}\t$centros{$chr_orig}->{q}->{start}\t.\t+\t.\tParent=$chr;Name=$chr\_cent\n/; }

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# BUGS

Please report them.

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# SEE ALSO

the Bio::Graphics::Panel manpage, the Bio::Graphics::Glyph manpage, the Bio::Graphics::Glyph::arrow manpage, the Bio::Graphics::Glyph::cds manpage, the Bio::Graphics::Glyph::crossbox manpage, the Bio::Graphics::Glyph::diamond manpage, the Bio::Graphics::Glyph::dna manpage, the Bio::Graphics::Glyph::dot manpage, the Bio::Graphics::Glyph::ellipse manpage, the Bio::Graphics::Glyph::extending_arrow manpage, the Bio::Graphics::Glyph::generic manpage, the Bio::Graphics::Glyph::graded_segments manpage, the Bio::Graphics::Glyph::heterogeneous_segments manpage, the Bio::Graphics::Glyph::line manpage, the Bio::Graphics::Glyph::pinsertion manpage, the Bio::Graphics::Glyph::primers manpage, the Bio::Graphics::Glyph::rndrect manpage, the Bio::Graphics::Glyph::segments manpage, the Bio::Graphics::Glyph::ruler_arrow manpage, the Bio::Graphics::Glyph::toomany manpage, the Bio::Graphics::Glyph::transcript manpage, the Bio::Graphics::Glyph::transcript2 manpage, the Bio::Graphics::Glyph::translation manpage, the Bio::Graphics::Glyph::triangle manpage, the Bio::DB::GFF manpage, the Bio::SeqI manpage, the Bio::SeqFeatureI manpage, the Bio::Das manpage, GD

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# AUTHOR

Gudmundur A. Thorisson <mummi@cshl.edu>

Copyright (c) 2001-2006 Cold Spring Harbor Laboratory

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# CONTRIBUTORS

Sheldon McKay <mckays@cshl.edu

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.

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Bio::Graphics::Glyph::ideogram - The "ideogram" glyph