ecotaxstat : getting the coverage of an ecoPCR output compared to the original ecoPCR database

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

-r TAXID, --required=<TAXID>

Taxids can be specified to focus the coverage on a smaller part of the taxonomy.

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.