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

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