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.TH "ECOTAXSTAT" "1" "Jul 27, 2019" " 1.02 13" "OBITools"
.SH NAME
ecotaxstat \- description of ecotaxstat
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The \fI\%ecotaxstat\fP command requires two parameters : an \fIecoPCR\fP formatted database (specified 
with the \fI\-d\fP option, (see obiconvert for a description of the database format) 
and an ecoPCR output (ideally computed using the specified ecoPCR database).
.sp
The command outputs, for every rank, the coverage (Bc) of the ecoPCR output. The coverage (Bc) is the 
fraction of \fItaxids\fP that have a sequence in the database and have also have a sequence in the ecoPCR 
output file.
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Optionally, \fItaxids\fP can be specified to focus the coverage on a smaller part of the taxonomy.
.SH ECOTAXSTAT SPECIFIC OPTIONS
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.B \-r TAXID, \-\-required=<TAXID>
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Taxids can be specified to focus the coverage on a smaller part of the taxonomy.
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\fIExample:\fP
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.ft C
> ecotaxstat \-d my_ecopcr_database seq.ecopcr
.ft P
.fi
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.sp
This command will print taxonomy coverage for the considered primer pair
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.SH TAXONOMY RELATED OPTIONS
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.B \-d <FILENAME>, \-\-database=<FILENAME>
ecoPCR taxonomy Database name
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.B \-t <FILENAME>, \-\-taxonomy\-dump=<FILENAME>
NCBI Taxonomy dump repository name
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.SH COMMON OPTIONS
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.B \-h, \-\-help
Shows this help message and exits.
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.B \-\-DEBUG
Sets logging in debug mode.
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.SH AUTHOR
The OBITools Development Team - LECA
.SH COPYRIGHT
2019 - 2015, OBITool Development Team
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