Support selecting multiple sequence sets to blast against - Githubissues

GMOD / mimosa

Miniature Model Organism Sequence Aligner

http://gmod.github.com/mimosa/

Artistic License 2.0

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Support selecting multiple sequence sets to blast against #37

Closed leto closed 13 years ago

rbuels commented 13 years ago

Check box in the first column of the sequence set grid. User checks the boxes for the sequence sets that they want to align against. Or something like that.

leto commented 13 years ago

User selects multiple mimosa_sequence_sets, controller checks if this combination of seqset's already exists on disk, if not, creates them by concatenating them all and passing that to Bio::GMOD::Database.

leto commented 13 years ago

Modify ExtJS grid to send all selected sequence sets to the form, instead of only the first
When a multi sequence set request comes in, we:
- Error out if any of the mimosa_sequence_set_id's we were given are invalid
- sort the list of sequence sets alphabetically by their content SHA1s
- take the SHA1 of this sorted list of SHA1s, this will be the unique key of this unioned set
- see if a cached version of this unioned set exists already, i.e. -e t/data/SHA1.seq
- If it does, use it
- If not, concatenate all the *.seq files for each sequence set, and save it in the file t/data/SHA1.seq
- Hand off to Bio::GMOD::Database

leto commented 13 years ago

Where is the best place to store the sha1 of the unioned/composite sequence set? The database or the filesystem?

leto commented 13 years ago

Consensus is that we will use the sha1 column on the mimosa sequence set table, which was just added in the multiseq branch.

leto commented 13 years ago

Modification: we will sort the mimosa_sequence_set_ids in increasing id order instead of by their names. We just need a specific ordering, and this one obviates the need to grab all the names from the database, then sort them.