On Tue, Nov 8, 2011 at 9:57 PM, Austin Paul <[email protected]> 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
