[Biopython] Reading from stdin with Bio.SeqIO
Brad Chapman
chapmanb at 50mail.com
Thu Jun 4 12:47:20 EDT 2009
Hi Giles;
You are very welcome in Python-land.
> I need to convert a solexa format fastq file into a sanger format fastq
> file.
[...]
> Unfortunately I can't find any documentation on how to read from or write to
> Unix pipes with Bio.SeqIO.
> Can anyone help?
You want to use sys.stdin and sys.stdout, which provide file handles
to standard in and out:
import sys
from Bio import SeqIO
recs = SeqIO.parse(sys.stdin, "fastq-solexa")
SeqIO.write(recs, sys.stdout, "fastq")
It would be great if you wanted to add this as an example in the
Cookbook documentation:
http://biopython.org/wiki/Category:Cookbook
Hope this helps,
Brad
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