[Biopython] SeqIO.convert
Brad Chapman
chapmanb at 50mail.com
Sun Nov 15 14:38:55 UTC 2009
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
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