[Bioperl-l] Creating a fastq format file?

[Dan Bolser]

In the Bio::SeqIO::fastq page:

http://search.cpan.org/~cjfields/BioPerl-1.6.0/Bio/SeqIO/fastq.pm#write_seq


I read:

"This object can transform Bio::Seq and Bio::Seq::Quality objects to
and from fastq flat file databases."

I'm not sure how to code the link between the fastq IO object and the
qual object that I have created using the code from the previous
thread...

Any suggestions? What am I missing?


2009/4/22 Dan Bolser <dan.bolser at gmail.com>:
> Creating a fastq format file from fasta and 'fasta quality file'?
>
>
> Hi,
>
> I'm sure this is easy, but I'm still not able to 'think bioperl'...
>
> I have a 'fasta quality file' and a fasta file, and I would like to
> output a fastq file. I followed the discussion on the previous thread
> here:
>
> http://bioperl.org/pipermail/bioperl-l/2008-July/028013.html
>
>
> With the conclusion seeming to be 'just do it'. Could someone point me
> at a way to do this, or was that suggestion an error? i.e. the poster
> was working out a way to create a fastq the only way possible...
>
> I get the feeling that this should be a one-liner, but perhaps the
> above thread was demonstrating the code I need to copy.
>
>
> Thanks for any suggestions,
>
> Dan.
>