[BioRuby] reading fastq files

[George Githinji]

I am trying out the current bioruby snapshot from github ....
which i have compiled as a local gem version 1.3.1.5000

There seems to be a number of changes and file re-naming from the current
stable release 1.3.1.
How do i parse a fastq file format?
I am getting an error while trying to read a fastq file.

#Read a fastq file
fastq = "/home/george/Assembly_pipeline/data/Sort.caf.fastq"
Bio::Fastq.new(fastq) do |f|
  f.each do |entry|
    puts entry.class
  end
end


Error: /home/george/NetBeansProjects/contig_assembly/lib/assemble_raw_read.rb:6:
no such file to load -- bio/db/fastq (LoadError)

Replacing the above with a call to Bio::FlatFile.auto does not seem to help
either. I have feeling am making a stupid mistake somewhere
or doing it the wrong way....
any ideas?


Thank you
George



-- 
---------------
Sincerely
George

Skype: george_g2
Blog: http://biorelated.wordpress.com/