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?


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
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


Reply via email to