[BioRuby] reading fastq files

[Naohisa Goto]

Hi,

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

In that case, updating of the file bioruby.gemspec would be
needed, "rake regemspec" in your local git repository.
The file bioruby.gemspec contains the list of files to be
stored to the gem, but it isn't frequently updated.

> 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|

  Bio::FlatFile.open(fastq) do |f|

Bio::Fastq.new takes a String of FASTQ entry, not filename.


>   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?

Please update to the newest snapshot and try again.

> 
> 
> Thank you
> George
> 
> 
> 
> -- 
> ---------------
> Sincerely
> George
> 
> Skype: george_g2
> Blog: http://biorelated.wordpress.com/
> _______________________________________________
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-- 
Naohisa Goto <ngoto at gen-info.osaka-u.ac.jp>