On Thu, Feb 16, 2012 at 10:47 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Wed, Feb 15, 2012 at 6:07 PM, Dannon Baker <dannonbaker@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...
Refactoring lib/galaxy/datatypes/sequence.py split method here, https://bitbucket.org/peterjc/galaxy-central/changeset/762777618073 This is part of a work-in-progress "split_blast" branch to try splitting BLAST jobs, for which I will need to split FASTA files as inputs, and also merge BLAST XML output: https://bitbucket.org/peterjc/galaxy-central/src/split_blast Peter