[Bioperl-l] Next-gen modules

Peter Cock p.j.a.cock at googlemail.com
Thu Jul 23 11:31:13 UTC 2009

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:


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:


Peter Rice and I have also been talking about line wrapping when
writing FASTQ output, and if this is a good idea or not:


Peter C. (@Biopython)

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