Create BLAST tabular adapter

[garrettjstevens]

This adds a synteny adapter that works with files generated by BLAST usint the -outfmt 6 option (called "tabular" output in the docs).

You can see a demo of this branch here: https://s3.amazonaws.com/jbrowse.org/code/jb2/create_blast_tabular_adapter/index.html?config=test_data%2Fgrape_peach_synteny%2Fconfig.json&session=share-4SDMC98yDL&password=JI48K

The demo file is just matches for the first 1,000,000 bases of Pp05 for peach and chr18 for grape. The file was generated like this:

# The files we have are Ppersica_Pp05_subset.fa and Vvinifera_chr18_subset.fa,
# both of with are the first 1,000,000 bases of the indicated chromosomes.
makeblastdb -in Vvinifera_chr18_subset.fa -dbtype nucl
tblastx -query Ppersica_Pp05_subset.fa -db Vvinifera_chr18_subset.fa -outfmt 6 -evalue 0.1 > peach_vs_grape.tsv

This took ~1m15s to generate on my computer.

[cmdcolin]

I rebased this off main and gzipped the sample data file in case you get merge conflicts when pulling!

[garrettjstevens]

Here's a new share link with the gene tracks: https://s3.amazonaws.com/jbrowse.org/code/jb2/create_blast_tabular_adapter/index.html?config=test_data%2Fgrape_peach_synteny%2Fconfig.json&session=share-csnO59YS7_&password=wSNlc

I also added a config option so users can specify their columns in case they used the custom column option in BLAST's outfmt. If you ran the command with -outfmt "6 qseqid sseqid qstart qend sstart send", then you would specify the columns in the config as 'qseqid sseqid qstart qend sstart send'. Those six columns are required, all others are optional.

[cmdcolin]

if you get a chance, i would be curious how outfmt 17 (SAM, then convert to BAM) works in jbrowse too...

[garrettjstevens]

outfmt 17 only works with blastn, so I've attached both the outfmt 6 file and outfmt 17 file using blastn. For some reason the raw SAM output has Query_1 instead of PP05, so I replaced it and converted to BAM, and those files are attached, too.

Here's what it looks like with outfmt 6 loaded as a synteny track and outfmt 17 loaded as an alignments track:

peach_vs_grape.blastn.tar.gz