gitax
v0.0.6
Published
from NCBI gi to taxonomy id
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gitax
gitax fetches taxonomy_id,names from given NCBI gi.
installation
$ npm install -g gitax
usage
command line
gi=1234567
tax_id=$(gitax $gi /path/to/gi_tax_nucl.dmp)
echo $tax_id
with taxonomy names
gi=1234567
gitax $gi /path/to/gi_tax_nucl.dmp --names /path/to/names.dmp
set default files
gitax_set /path/to/gi_tax_nucl.dmp --names /path/to/names.dmp
# run without gi_tax_nucl
gitax 1234567
# unset
gitax_set
JavaScript API
gitax = require("gitax")
tax_id = gitax(1234567, "/path/to/gi_tax_nucl.dmp");
with taxonomy names
gitax = require("gitax")
taxinfo = gitax(1234567, "/path/to/gi_tax_nucl.dmp", "/path/to/names.dmp");
console.log(taxinfo.tax_id); // taxonomy id
console.log(taxinfo.names); // taxonomy names // array of [name, uniq_name, name_class]
gi_tax_nucl.dmp?
a file which describes relations between gi and taxonomy_id
download one from ftp://ftp.ncbi.nih.gov/pub/taxonomy/
names.dmp?
a file which describes relations between gi and taxonomy_id
downloaded with gi_tax_nucl.dmp (from ftp://ftp.ncbi.nih.gov/pub/taxonomy/)
wget -r ftp://ftp.ncbi.nih.gov/pub/taxonomy/