On Wed, Feb 15, 2012 at 6:07 PM, Dannon Baker <dannonba...@me.com> wrote:
> Good luck, let me know how it goes, and again - contributions are certainly
> welcome :)

I think I found the first bug, method split in lib/galaxy/datatypes/sequence.py
for class Sequence assumes four lines per sequence. This would make
sense as the split method of the Fastq class (after grooming to remove
any line wrapping) but is a very bad idea on most sequence file formats
(e.g. FASTA).

It looks like a little refactoring is needed, defining a Sequence split method
which raises not implemented, and moving the current code to the Fastq
class, then writing something similar but allowing multiple lines per record
for the Fasta class.

Does that sound reasonable? I'll do this on a new branch for review...

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