Hi Peter,

Thanks for the suggestion.  For example, I have a fastq file with 50
million reads and I want to randomly select 5 million of them.  It seems
biopython would very easily select a single or a handful of reads with the
Bio.SeqIO.index() function.  Would it also be able to do the job I am
interested in?

Austin

On Tue, Nov 8, 2011 at 2:07 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Tue, Nov 8, 2011 at 9:57 PM, Austin Paul <austi...@usc.edu> wrote:
> > Hi,
> >
> > I am curious if anyone knows how to select random lines from a fastq
> file.
> > There is a select random lines tool in text manipulation tools, but it
> does
> > not treat fastq files specifically, so it will not group quality lines
> with
> > sequence lines.  And if I turn the fastq file to tabular form in order to
> > select lines, I can no longer return it to fastq form.  Anyone know a
> way to
> > do this in galaxy?  Otherwise, perhaps another program?  Thanks.
> >
> > Austin
>
> How big are your FASTQ files (can they be indexed in memory)?
>
> And are you willing to program? If you like Python, Biopython's
> Bio.SeqIO.index(...) or Bio.SeqIO.index_db(...) functions would
> let you do this easily. Have a look at the "Getting the raw data
> for a record" example in the tutorial, and please ask if you liked
> a little more help:
> http://biopython.org/DIST/docs/tutorial/Tutorial.html
> http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
>
> Regards,
>
> Peter
>
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