[Bioperl-l] Next-gen modules

Peter biopython at maubp.freeserve.co.uk
Fri Jul 24 05:28:44 EDT 2009

On Thu, Jul 23, 2009 at 11:58 PM, Chris Fields<cjfields at illinois.edu> wrote:
>> i.e. Something like this four line Biopython script would be perfect:
>> http://biopython.org/wiki/Reading_from_unix_pipes
> We use named parameters so it's a little more verbose.
> use Bio::SeqIO;
> my $in  = Bio::SeqIO->new(-fh => \*STDIN, -format => 'fastq-sanger');
> my $out = Bio::SeqIO->new(-format => 'fastq-solexa');
> while (my $seq = $in->next_seq) { $out->write_seq($seq) }

Thanks. So that implicitly uses STDOUT for the output?

> Don't be surprised if there are still bugs lurking about, just let me know
> and I'll fix 'em.

Have you guys (BioPerl) have also gone for "fastq-sanger" instead of
just "fastq" for the Sanger Standard version of FASTQ (like EMBOSS)?
Does BioPerl use just "fastq" to mean anything?

If BioPerl and EMBOSS are using "fastq-sanger", I think Biopython will
have to support that as an alias too:



More information about the Bioperl-l mailing list