--- name: "ecotaxstat" section: "1" platform: "linux" package: "obitools" version: "1.2.12+dfsg-2" release: "Debian 10 (Buster)" platforms: ["linux"] url: "https://new.carta.tech/ecotaxstat" --- # ecotaxstat(1) 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. ## 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=\** 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 \, --database=\** ecoPCR taxonomy Database name - **-t \, --taxonomy-dump=\** 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