NCBI-taxcollector Main Functions

NCBI-taxcollector Main Functions is a tool for using the GI field of the FASTA format to search taxonomy information in NCBI bases. It is designed to maximize performance and allow many searches per second. It runs as a command line tool and, for this reason, it is especially suitable for use in scripts.

Examples of usage

Searching the tax tree for a given gi:

$ time ./ncbitc -s 2
9913 | 9903 | species | BT | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 0 |  |
9903 | 27592 | genus |  | 2 | 1 | 1 | 1 | 2 | 1 | 0 | 0 |  |
27592 | 9895 | subfamily |  | 2 | 1 | 1 | 1 | 2 | 1 | 0 | 0 |  |
9895 | 35500 | family |  | 2 | 1 | 1 | 1 | 2 | 1 | 0 | 0 |  |
35500 | 9845 | infraorder |  | 2 | 1 | 1 | 1 | 2 | 1 | 0 | 0 |  |
9845 | 91561 | suborder |  | 2 | 1 | 1 | 1 | 2 | 1 | 0 | 0 |  |
91561 | 314145 | no rank |  | 2 | 1 | 1 | 1 | 2 | 1 | 0 | 0 |  |
314145 | 9347 | superorder |  | 2 | 1 | 1 | 1 | 2 | 1 | 0 | 0 |  |
9347 | 32525 | no rank |  | 2 | 1 | 1 | 1 | 2 | 1 | 0 | 0 |  |
32525 | 40674 | no rank |  | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 0 |  |
40674 | 32524 | class |  | 2 | 0 | 1 | 1 | 2 | 1 | 0 | 0 |  |
32524 | 32523 | no rank |  | 10 | 1 | 1 | 1 | 2 | 1 | 1 | 0 |  |
32523 | 8287 | no rank |  | 10 | 1 | 1 | 1 | 2 | 1 | 1 | 0 |  |
8287 | 117571 | no rank |  | 10 | 1 | 1 | 1 | 2 | 1 | 1 | 0 |  |
117571 | 117570 | no rank |  | 10 | 1 | 1 | 1 | 2 | 1 | 0 | 0 |  |
117570 | 7776 | no rank |  | 10 | 1 | 1 | 1 | 2 | 1 | 1 | 0 |  |
7776 | 7742 | superclass |  | 10 | 1 | 1 | 1 | 2 | 1 | 1 | 0 |  |
7742 | 89593 | no rank |  | 10 | 0 | 1 | 1 | 2 | 1 | 0 | 0 |  |
89593 | 7711 | subphylum |  | 10 | 0 | 1 | 1 | 2 | 0 | 0 | 0 |  |
7711 | 33511 | phylum |  | 1 | 1 | 1 | 1 | 5 | 1 | 0 | 0 |  |
33511 | 33316 | no rank |  | 1 | 1 | 1 | 1 | 5 | 1 | 1 | 0 |  |
33316 | 33213 | no rank |  | 1 | 1 | 1 | 1 | 5 | 1 | 1 | 0 |  |
33213 | 6072 | no rank |  | 1 | 1 | 1 | 1 | 5 | 1 | 1 | 0 |  |
6072 | 33208 | no rank |  | 1 | 1 | 1 | 1 | 5 | 0 | 1 | 0 |  |
33208 | 33154 | kingdom |  | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 0 |  |
33154 | 2759 | no rank |  | 4 | 0 | 1 | 1 | 1 | 1 | 1 | 0 |  |
2759 | 131567 | superkingdom |  | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 |  |

real	0m0.002s
user	0m0.000s
sys		0m0.000s

Searching all name entries for a given tax id:

$ ./ncbitc -n 9913
9913 |  Bos Tauurus |  |  misspelling |
9913 |  Bos bovis |  |  synonym |
9913 |  Bos primigenius taurus |  |  synonym |
9913 |  Bos taurus |  |  scientific name |
9913 |  Bovidae sp. Adi Nefas |  |  includes |
9913 |  bovine |  |  common name |
9913 |  cattle |  |  genbank common name |
9913 |  cow |  |  common name |
9913 |  domestic cattle |  |  common name |
9913 |  domestic cow |  |  common name |

real	0m0.001s
user	0m0.000s
sys	0m0.000s

Installing

Download and build the program:

git clone git://github.com/mvneves/ncbitaxcollector
cd ncbitaxcollector
make

Download gi_taxid_nucl.dmp, names.dmp and nodes.dmp from NCBI's FTP site:

wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
tar -xzf taxdump.tar.gz

References

• NCBI Taxonomy tree in SQL: http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap/downloads/ncbi/
• A TaxCollector in python: https://github.com/audy/taxcollector