[Bioperl-l] Next-gen modules

[Peter Cock]

On Wed, Jul 8, 2009 at 5:24 PM, Chris Fields<cjfields at illinois.edu> wrote:
>
> It would be nice to get some regression tests going for this to make sure it
> does what we expect, so maybe some test data and expected results?
>

Regression tests for BioPerl's FASTQ support would of course
be sensible. In terms of sample data and expected results...

I've got some test files put together for Biopython, and I have
been cross checking Biopython's FASTQ support against
EMBOSS 6.1.0 which has turned up a few issues:
http://lists.open-bio.org/pipermail/emboss-dev/2009-July/000577.html

------------------------------------------------------------------------------

I'd like to get comparisons against BioPerl's new FASTQ support
going too. To do this I'd need to know which (branch?) of BioPerl I
should install, and I'd also like a trivial sample BioPerl script to do
piped FASTQ conversion. i.e. read a FASTQ file from stdin (say
as "fastq-solexa"), and output it to stdout (say as "fastq" meaning
the Sanger Standard FASTQ).

i.e. Something like this four line Biopython script would be perfect:
http://biopython.org/wiki/Reading_from_unix_pipes

------------------------------------------------------------------------------

Peter Rice and I have also been talking about line wrapping when
writing FASTQ output, and if this is a good idea or not:
http://lists.open-bio.org/pipermail/emboss-dev/2009-July/000593.html

Thanks!

Peter C. (@Biopython)