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bio-synreport.gemspec

README.rdoc

bio-synreport

A gem that takes gene CDS sequences and GFF as input. From this a database is created and the user can interrogate the database object.The user may then pass a chromosome ID, a position and an alternative nucleotide. The database will return information about whether the suggested substitution creates a synonymous or non-synonymous substitution, and the identity of the changes as a hash with many attributes.

For example,

	 db = Bio::Util::SynReport.new(:gff => 'some_gff.gff', :fasta => 'some_cds.fa', :verbose => true)
	 chr, pos, ref,alt = 'Chr2', 15973794, 'C', 'T'
	 pp db.mutation_info(chr,pos,alt)

Would return something like,

{
:chr => 'Chr2', 
:strand => '-', 
:position => 15973794,
:original_codon => 'atg', 
:original_residue => 'Met', 
:mutant_codon => 'ttg', 
:mutant_residue => 'Lys', 
:position_in_codon => 1, 
:substitution_type => 'NON_SYN'
 }

To Do

The module isn't the fastest thing in the world. Needs much speeding up…

Contributing to bio-synreport

  • Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet

  • Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it

  • Fork the project

  • Start a feature/bugfix branch

  • Commit and push until you are happy with your contribution

  • Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.

  • Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.

Copyright

Copyright © 2012 Dan MacLean. See LICENSE.txt for further details.