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| ECOFIND(1) | OBITools | ECOFIND(1) |
NAME¶
ecofind - description of ecofind
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.
AUTHOR¶
The OBITools Development Team - LECA
COPYRIGHT¶
2019 - 2015, OBITool Development Team
| January 21, 2019 | 1.02 12 |