Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Browse files

added usage in readme

  • Loading branch information...
commit 0ec7eb35a5d9ca2231669191b340e9efdcc28a87 1 parent eabf4c7
@chmille4 authored
Showing with 40 additions and 2 deletions.
  1. +40 −2 README.rdoc
View
42 README.rdoc
@@ -10,8 +10,46 @@ gem install bio-assembly
== Usage
-Examples on my blog:
-http://chasemiller4.blogspot.com/2010/10/bioruby-ace-parser-example.html
+ require 'bio-assembly'
+
+ # ace file path
+ asm = Bio::Assembly.new("data.ace", :ace)
+
+ # iterate through contigs (streams each contig)
+ asm.each_contig do |contig|
+
+ # print name and consensus seq
+ puts contig.name
+ puts contig.consensus_seq
+
+ # iterate through reads
+ contig.each_read do |read|
+
+ # print name, sequence and orientation
+ puts read.name
+ puts read.seq
+ puts read.orientation
+
+ # print the postion of the read
+ # in relation to the consensus seq
+ puts read.from
+ puts read.to
+
+ # print the portion of the read
+ # that was used to create the consensus
+ puts read.clear_range_from
+ puts read.clear_range_to
+
+ end
+
+ # grab the reads that make up a particular region of the contig
+ reads_in_region = contig.find_reads_in_range(10, 50)
+
+ end
+
+ # experimental - output ace
+ file = File.new('out.ace', 'w')
+ file.puts asm.to_ace
== Contributing to bio-assembly
Please sign in to comment.
Something went wrong with that request. Please try again.