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
io | [R] |
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