[BioPython] Feedback from Biopython 1.50 beta?

[Peter]

On Mon, Apr 13, 2009 at 7:15 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Support for reading/writing FASTQ and QUAL files is also new - if
> you've tried it out on your own second generation sequencing files,
> again, it would be nice to know how it worked.  If everything is fine,
> great, but if for example it can't parse the files from your local
> sequencing center, please let us know.

David Schruth emailed to let me know he's successfully been using the
new QUAL functionality in Bio.SeqIO on 454 data.  Thanks David!

There isn't much in the main Biopython tutorial on this yet, but in
the meantime have a look at the built in documentation for our FASTQ
and QUAL support:
>>> from Bio import SeqIO
>>> help(SeqIO.QualityIO)
...

For those that didn't know, the Roche 454 off instrument applications
(available on Linux only I believe) include a command line tool called
"sffinfo" which can convert a binary SFF file into FASTA (using the
command line option -s or -seq) or QUAL format using PHRED qualities
(command line option -q or -qual).  I've been using this myself to get
some Roche 454 SFF read data into Bio.SeqIO in order to manually trim
off primer sequences.

Peter