On Feb 16, 2012, at 12:24 PM, Peter Cock wrote:

> On Thu, Feb 16, 2012 at 4:28 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> Hi Dan,
>> I think I need a little more advice - what is the role of the script
>> scripts/extract_dataset_part.py and the JSON files created
>> when splitting FASTQ files in lib/galaxy/datatypes/sequence.py,
>> and then used by the class' process_split_file method?
>> Why is there no JSON file created by the base data class in
>> lib/galaxy/datatypes/data.py and no method process_split_file?
>> Is the JSON thing part of a partial and unfinished rewrite of the
>> splitter code?
>> On the assumption that not all splitters bother with the JSON,
>> I am trying a little hack to scripts/extract_dataset_part.py to
>> abort silently if there is no JSON file:
>> https://bitbucket.org/peterjc/galaxy-central/changeset/ebe94a2c25c3
>> This seems to be working with my current attempt at a FASTA
>> splitter (not checked in yes, only partly implemented and tested).
> I've checked in my FASTA splitting, which now seems to be
> working OK with my BLAST tests. So far this only does splitting
> into chunks of the requested number of sequences, rather than
> the option to split the whole file into a given number of pieces.
> https://bitbucket.org/peterjc/galaxy-central/changeset/416c961c0da9

Cool!  Seems like a perfectly fine start.  I guess you could grab the # of 
sequences from the dataset somehow (I'm guessing that is set somehow upon 
import into Galaxy).

> I also need to look at merging multiple BLAST XML outputs, but
> this is looking promising.
> Peter

Yep, that's definitely one where a simple concatenation wouldn't work (though 
NCBI used to think so, years ago…)

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