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

       -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.

AUTHOR

       The OBITools Development Team - LECA

COPYRIGHT

       2019 - 2015, OBITool Development Team

 1.02 12                                   Jan 28, 2019                             ECOTAXSTAT(1)