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.cock@googlemail.comwrote:
On Tue, Nov 8, 2011 at 9:57 PM, Austin Paul austinpa@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