[BioRuby] reading fastq files

[George Githinji]

Hi all,
It seems that the bioruby.gemspec file did not include the following lines
when building the initial gem
"lib/bio/db/fasta/fasta_to_biosequence.rb",
    "lib/bio/db/fastq/fastq_to_biosequence.rb",
    "lib/bio/db/fastq/format_fastq.rb",
    "lib/bio/db/fastq.rb",
    "lib/bio/db/sanger_chromatogram/abif.rb",
    "lib/bio/db/sanger_chromatogram/chromatogram.rb",
    "lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb",
    "lib/bio/db/sanger_chromatogram/scf.rb",
    "lib/bio/db/phyloxml/phyloxml.xsd",
    "lib/bio/db/phyloxml/phyloxml_elements.rb",
    "lib/bio/db/phyloxml/phyloxml_parser.rb",
    "lib/bio/db/phyloxml/phyloxml_writer.rb",
    "lib/bio/sequence/quality_score.rb",

Upon adding the above lines to the bioruby.gemspec and rebuilding the gem,
the functionality is now available.


>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 16 Dec 2009 14:37:45 +0300
> From: George Githinji <georgkam at gmail.com>
> Subject: [BioRuby] reading fastq files
> To: bioruby at lists.open-bio.org
> Message-ID:
>        <55915f820912160337g3aa1121fv55ded38f8802bd7f at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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/
>
>
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> End of BioRuby Digest, Vol 51, Issue 1
> **************************************
>



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

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