[Bioperl-l] Creating a fastq format file?

Dan Bolser dan.bolser at gmail.com
Wed Apr 22 09:32:15 EDT 2009

In the Bio::SeqIO::fastq page:


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

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.

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