Generate allele images in a specified format from a genomic data. By default the genomic data will be in GenBank format and the images will be rendered in PNG format.
Only 10 “TYPE”s of things are in our cassette regions:
[
'SSR_site', 'polyA_site', 'misc_feature', 'gateway', 'gene', 'LRPCR_primer', 'intron', 'primer_bind', 'promoter', 'PCR_primer', 'exon'
]
How many of these are we interested in displaying (probably all). What do we want to display in each case. Which of these are “main” features and which are “annotation” features?
Based on www.sanger.ac.uk/htgt/report/gene_report?project_id=47462, we may have to change the way we process the rows and sections. It may mean that we do not have to separate the annotation features from the main features. We should just not consider the annotation features when we are calculating the widths of sections.
Bill has an example of what the images should look like in the link below. Develop the images to that specification:
www.knockoutmouse.org/about/view-all-ikmc-allele-types
-------- ----------
INPUT -> / parser / -> CONSTRUCT -> / renderer / -> OUTPUT
-------- ----------
(new selects the INPUT parser and the render displays the image in the OUTPUT format)
CONSTRUCT could be a JSON string, Ruby Hash, or perhaps a more sophisticated object. It should have the following attributes:
:features => [ { :name, :type, :start, :stop } ]
:circular => Bool
:label => String
It should perhaps also have the following (have not decided) attributes as well OR :features should be split into the following groups:
:cassette :backbone :five_arm :three_arm :five_flank :three_flank
The renderer has to decide on how to navigate the features and render it to the given format based on these attributes. The defaults for INPUT and OUTPUT are GenBank and PNG respectively.
The code layout should be something like the following:
CONSTRUCT::IMAGE CONSTRUCT::RENDERABLE_FEATURES CONSTRUCT::PARSER::INPUT CONSTRUCT::RENDERER::OUTPUT
That way, when we want to create a new CONSTRUCT::IMAGE object, it selects the PARSER and RENDERER to use based on the specified INPUT and OUTPUT formats:
CONSTRUCT::IMAGE.new( DATA [, { optional arguments }] ) -> CONSTRUCT::IMAGE
When we call the render method, an image in the OUTPUT format gets generated.
CONSTRUCT::IMAGE.new( DATA ).render() -> OUTPUT
Any RENDERER should be able to render all the features listed in a configuration file or schema (RENDERABLE_FEATURES). How it handles these are up to the RENDERER. Any features not on this list should be ignored (with a warning). Perhaps the RENDERER should be a mixin?
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Render images in various formats (PNG, SVG, Text)
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Accept data from different sources (GenBank file, database)
require "allele_image" allele_image = AlleleImage::Image.new( "/path/to/genbank/file.gbk" ) magick_image = allele_image.render() # the image is a Magick::Image magick_image.write( "/path/to/image/file.png" )
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RMagick
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bioruby
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sudo gem install allele_image
(The MIT License)
Copyright © 2010 Genome Research Limited
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