read.names.sql for common names

[meixilin]

Hi,

Thanks for making this great package. I am wondering if there could be any SQL support for the common names? It will be nice if taxonomizr::getTaxonomy(ids = uids, sqlFile = mysql) could give an option for returning the common names in the NCBI taxonomy dump files, in addition/other than only scientific names.

Thank you!

[sherrillmix]

Hmm that's a good suggestion. We've got getId to go from common name to accession but not the inverse. I hadn't been keeping the name type column in the sqlite database so I'll have to add that back in so people can filter by "common name" or whatever name type they want.

I think I've got the rough framework set up. I'll take a poke at polishing it up this weekend and aim to get a version up on github soon.

[sherrillmix]

Got a bit sidetracked but this should be implemented in v0.9.4 now on github. For example:

getCommon(c(9913,9606),'accessionTaxa.sql')

## [[1]]
##                         name                type
## 1                  Bos bovis             synonym
## 2     Bos primigenius taurus             synonym
## 3  Bos taurus Linnaeus, 1758           authority
## 4                 Bos taurus     scientific name
## 5      Bovidae sp. Adi Nefas            includes
## 6                     bovine         common name
## 7                     cattle genbank common name
## 8                        cow         common name
## 9                  dairy cow         common name
## 10           domestic cattle         common name
## 11              domestic cow         common name
## 12                        ox         common name
## 13                      oxen         common name
## 
## [[2]]
##                          name                type
## 1 Homo sapiens Linnaeus, 1758           authority
## 2                Homo sapiens     scientific name
## 3                       human genbank common name