ecofind: querying a taxonomic database

ecofind retrive taxonomic information from taxonomic database given either a taxid or a regular expression patterns.

ecofind specific options

-d <filename>

Filename containing the database used for the in silico PCR. The database must be in the ecoPCR format (see obiconvert).

Warning

This option is compulsory.

-a

Enable the search on all alternative names and not only scientific names.

-L

List all taxonomic rank available for -r option and exit.

-r

Restrict to given taxonomic rank.

-s

Displays all subtree’s information for the given taxid.

-p

Displays all parental tree’s information for the given taxid.

-P

Display taxonomic Path as suplementary column in output

-h

Print help.

Output file

The output file contains several columns, with ‘|’ as separator, and describes the properties of the retrieved taxids.

column 1: the taxid

column 2: the taxonomic rank

column 3: the name (not only scientific)

column 4: class name

column 5: the scientific name

column 6 (optional): the full taxonomic path of the taxid

Examples

Example 1:

>  ecofind -d mydatabase 'homo ' > homo_.tax

Retrieve all taxids whose ‘homo ‘ is contained in the associated names.

Example 2:

> ecofind -d mydatabase  -p 9606 -P > sapiens.info.tax

Retrieve all parents taxa of the 9606 taxid. The -P option add a supplementary column with the full path for each taxid.