table of contents
| ECOTAXSTAT(1) | OBITools | ECOTAXSTAT(1) |
NAME¶
ecotaxstat - description of ecotaxstat
The ecotaxstat command requires two parameters : an ecoPCR formatted database (specified with the -d option, (see obiconvert for a description of the database format) and an ecoPCR output (ideally computed using the specified ecoPCR database).
The command outputs, for every rank, the coverage (Bc) of the ecoPCR output. The coverage (Bc) is the fraction of taxids that have a sequence in the database and have also have a sequence in the ecoPCR output file.
Optionally, taxids can be specified to focus the coverage on a smaller part of the taxonomy.
ECOTAXSTAT SPECIFIC OPTIONS¶
Example:
> ecotaxstat -d my_ecopcr_database seq.ecopcr
This command will print taxonomy coverage for the considered primer pair
TAXONOMY RELATED OPTIONS¶
- -d <FILENAME>, --database=<FILENAME>
- ecoPCR taxonomy Database name
- -t <FILENAME>, --taxonomy-dump=<FILENAME>
- NCBI Taxonomy dump repository name
COMMON OPTIONS¶
- -h, --help
- Shows this help message and exits.
- --DEBUG
- Sets logging in debug mode.
AUTHOR¶
The OBITools Development Team - LECA
COPYRIGHT¶
2019 - 2015, OBITool Development Team
| July 27, 2019 | 1.02 13 |