On Tue, Nov 8, 2011 at 10:26 PM, Austin Paul <austi...@usc.edu> wrote:
> 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

I think so, but you'd have to use Bio.SeqIO.index_db() which stores
the index in an SQLite dictionary rather than in memory which isn't
really viable here (unless you have a 64bit big memory machine?).
I don't think I've tried it with quite that many reads though...

Alternatively, if I understood her correctly, Jennifer pointed out you
can do this in Galaxy but it will take a lot of IO:

1. Convert FASTQ to tabular (4 lines per record -> 1 line per record)
2. Randomly select lines (each line is now a record so safe)
3. Convert tabular back to FASTQ

It should work though, and requires no additional programming.


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