Class Gmap::Core
In: lib/gmap/core.rb
Parent: Object

This module allows the parsing of the standard output of Gmap (www.gene.com/share/gmap/)

Example:

  Gmap::Core.open("output.gmap") do |gmap|

    gmap.each_sequence do |seq|

      seq.each do |result|

        result.query (Query sequence name)
        result.target  (Target sequence name)
        result.q_start (Start coordinate of the query sequence)
        result.q_end (End coordinate of the query sequence)
        result.start (Start coordintate of the target sequence)
        result.end (End coordinate of the target sequence)
        result.strand (Strand of the target sequence)
        result.exons (# exons found)
        result.coverage (Coverage of the query sequence)
        result.perc_identity (Pecentage of identity from the alignment)
        result.indels (# insertion or deletions)
        result.mismatch (# mismatch)
        result.aa_change (Prediction of AA changes from mismatches and indels found)
        result.aln (Raw alignment between target and query sequences)

        ONLY IF GENE MAPS ARE USED WITH GMAP

        result.gene_start (Start coordinate of the overlapping gene)
        result.gene_end (End coordinate of the overlapping gene)
        result.gene_id (ID of the overlapping gene)
      end

    end

  end

Methods

close   each_sequence   new   open  

Attributes

io  [R] 

Public Class methods

Open the gmap file for reading

Public Instance methods

Close the IO stream on the Gmap file

Iterates on every sequence processed by Gmap and returns an array of Gmap::Result objects each of them corresponding to a Path (result) for that sequence

[Validate]