Restore sequence retrieval under mouse cursor

[josiahseaman]

DDV originally had the ability to load the file from the server, then click on a particular spot and get the sequence from that position. This code was disabled during the design of TileLayout, but the inactivated code is all still there inside nucleotideNumber.js. This code needs to be reactivated and updated for the new FluentDNA feature set.

The main use case to optimize for is retrieving a 300bp sequence from a 1GB genome with multiple scaffolds. Changes might need to be made to handle multiple scaffolds, though currently the "nucleotide number" being output does match the character file position under the mouse cursor. Ideally, grabbing a small sequence should not require requesting the entire genome from the server (this is why the feature was removed in the first place). Instead, loading only the scaffold in question might be a healthy middle ground.

One static file solution would be to create a fasta directory and chunk the genome into 10MB chunks which could be retrieved independently. This would scale well with large genomes as well as draft genomes with millions of contigs. In Python, all the staging for this happens in TileLayout.output_fasta()

Unfortunately in my understanding, it's not possible to submit a dynamic query to the static file server we're using for FluentDNA. In terms of IO speeds, the use running the server locally and browsing a new private genome will be a fairly common use case.

Notes: It might help that in ContigSpacingJSON a contig.name will contain the name of the cursor contig found in nucleotide_coordinates_to_sequence_index(). #39 is relevant in that we are going to need to change ContigSpacingJSON formatting to list the name of the contig, then the local (rather than file) nucleotide index.

• Old functionality re enabled
• Fetching less than a full genome
• Chunking large chromosomes or dynamic query?

[josiahseaman]

TransposonLayout and MultipleAlignmentLayout (MSA) currently not supported.
TransposonLayout composes a source from many fragments.
MultipleAlignmentLayout source is multiple files (feature pending).

[josiahseaman]

5602fd0

Putting the mouse in the upper left corner gets you the first letter of the sequence with a look-back of the contig name. All whitespace has been scrubbed, which in this case looks a bit off. This is based on file coordinates. Contig coordinates are the next priority.