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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