Taxonomy information

[yeban]

Taxonomy data is relevant to many analyses. For example, to infer taxonomical composition of samples in metagenomic studies.

To get taxonomy data from BLAST:

1. Format database with -taxid option.
2. Download NCBI's taxonomy database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz) and put it in pwd (essentially the db should be in the directory from which you run BLAST).
3. Use -outfmt 6 (tabular) with relevant options to get taxonomy information.

TODOs

• [x] In the first step we will just want to make sure taxonomy info is available in full TSV download (currently taxonomy columns have N/A in it).
• [x] Then we include this information in the tabular overview per query of our HTML results.
• [ ] Then do a simple visualisation.

[yeban]

I was thinking we could visualise taxonomy information like a tree.

                                            |---- S. invicta   (8)
                     |---- Formicidae (19) -|
                     |                      |---- C. flordanus (11)
Hymenoptera (26) ----|
                     |                 |---- B. terrestris (3)
                     |---- Apidae (7)- |
                                       |---- A. mellifera (4)

• length of the edges don't mean anything
• number in parenthesis indicate number of hits per taxa
• one visual per query
• clicking on a taxa could filter hits

It may be possible to construct lineage from species name using taxdump.tar.gz from ftp://ftp.ncbi.nih.gov/pub/taxonomy/

[yeban]

Discussing visualisation in #249.