[Biopython] SeqIO.convert

[Brad Chapman]

Hello;

> I have to convert fastq to fasta and to trim the sequence. I have found 
> SeqIO.convert:
> 
> from Bio import SeqIO
> count = SeqIO.convert("a.fastq", "fastq", "a.fasta", "fasta")
> 
> But I do not know how can I trim the sequence.

SeqIO.convert is a format converter only, but you can use it along
with other Biopython modules to trim adaptors. Here's a description:

http://bcbio.wordpress.com/2009/08/09/trimming-adaptors-from-short-read-sequences/

along with code:

http://github.com/chapmanb/bcbb/blob/master/align/adaptor_trim.py

Hope this helps,
Brad