plot_karyogram
[plot_karyogram] to see which) and it is possible to depict chromosome positions based on Biopiece records in the stream. The output is SVG (Scalable Vector Graphics) and you need a SVG viewer to see the plot such as Firefox or Inskape (Inkscape can also be used to modify the resulting image).
Read more about Inkscape here:
... | plot_karyogram [options]
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-o <file> | --data_out=<file>] # Write result to file.
[-g <string> | --genome=<string>] # Genome layout of karyogram: hg18|mm9
[-f <string> | --feat_color=<string>] # Color of features - Default=black
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
To plot a karyogram with some positions indicated from a BED file, do:
read_bed -i test.bed | plot_karyogram -xg hg18 -o karyogram.svg
And the result will look like this:
[list_genomes]
[read_bed]
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
[plot_karyogram] is part of the Biopieces framework.