gitax
gitax fetches taxonomy_id,names from given NCBI gi.
installation
$ npm install -g gitax
usage
command line
gi=1234567tax_id=$(gitax $gi /path/to/gi_tax_nucl.dmp)echo $tax_id
with taxonomy names
gi=1234567gitax $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 = tax_id = ;
with taxonomy names
gitax = taxinfo = ;console; // taxonomy idconsole; // 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/