iimog
commented
6 years ago Libraries in other languages that already implement this feature:
- taxadb (python) → I could not get it to work with sqlite though
- taxonomizr (R) → I got an error trying to init the db though (probably my own fault, I'll investigate)
I tried in `/tmp/` as working directory:
```R
library(taxonomizr)
getNamesAndNodes()
getAccession2taxid(type="nucl_gb")
read.accession2taxid(list.files('.','accession2taxid.gz$'),'accessionTaxa.sql')
```
this resulted in the following error:
```
Reading nucl_gb.accession2taxid.gz.
Reading in values. This may take a while.
Error: Problem creating sql file. Deleting.
Error in connection_import_file(conn@ptr, name, value, sep, eol, skip) :
RS_sqlite_import: /tmp/RtmpvgISg2/file6e4460728c25 line 113360323 expected 2 columns of data but found 1
```
The referenced file seems to be truncated in line 113360323 (it ends after the accession with no line break).
greatfireball
NCBI decided to phase out gi numbers in favour of accession numbers: https://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/ This module heavily relies on gi numbers and might not work with more recent ncbi taxonomy dumps. Functions to use accessions rather than gi numbers need to be implemented.