.\" Man page generated from reStructuredText.
.
.TH "ECODBTAXSTAT" "1" "Jul 27, 2019" " 1.02 13" "OBITools"
.SH NAME
ecodbtaxstat \- description of ecodbtaxstat
.
.nr rst2man-indent-level 0
.
.de1 rstReportMargin
\\$1 \\n[an-margin]
level \\n[rst2man-indent-level]
level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
-
\\n[rst2man-indent0]
\\n[rst2man-indent1]
\\n[rst2man-indent2]
..
.de1 INDENT
.\" .rstReportMargin pre:
. RS \\$1
. nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin]
. nr rst2man-indent-level +1
.\" .rstReportMargin post:
..
.de UNINDENT
. RE
.\" indent \\n[an-margin]
.\" old: \\n[rst2man-indent\\n[rst2man-indent-level]]
.nr rst2man-indent-level -1
.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]
.in \\n[rst2man-indent\\n[rst2man-indent-level]]u
..
.sp
The \fI\%ecodbtaxstat\fP command requires an \fBecopcr\fP database and a taxonomic rank 
(specified by the \fB\-\-rank\fP option, default \fIspecies\fP). The command outputs first 
the total number of sequence records in the database having taxonomic information at this rank, 
and then the number of sequence records for each value of this rank.
.SH ECODBTAXSTAT SPECIFIC OPTION
.INDENT 0.0
.TP
.B \-\-rank=<TAXONOMIC_RANK>
The taxonomic rank at which frequencies have to be computed.
Possible values are:
.INDENT 7.0
.INDENT 3.5
.INDENT 0.0
.IP \(bu 2
class
.IP \(bu 2
family
.IP \(bu 2
forma
.IP \(bu 2
genus
.IP \(bu 2
infraclass
.IP \(bu 2
infraorder
.IP \(bu 2
kingdom
.IP \(bu 2
order
.IP \(bu 2
parvorder
.IP \(bu 2
phylum
.IP \(bu 2
species           (default)
.IP \(bu 2
species group
.IP \(bu 2
species subgroup
.IP \(bu 2
subclass
.IP \(bu 2
subfamily
.IP \(bu 2
subgenus
.IP \(bu 2
subkingdom
.IP \(bu 2
suborder
.IP \(bu 2
subphylum
.IP \(bu 2
subspecies
.IP \(bu 2
subtribe
.IP \(bu 2
superclass
.IP \(bu 2
superfamily
.IP \(bu 2
superkingdom
.IP \(bu 2
superorder
.IP \(bu 2
superphylum
.IP \(bu 2
tribe
.IP \(bu 2
varietas
.UNINDENT
.UNINDENT
.UNINDENT
.UNINDENT
.SH TAXONOMY RELATED OPTIONS
.INDENT 0.0
.TP
.B \-d <FILENAME>, \-\-database=<FILENAME>
ecoPCR taxonomy Database name
.UNINDENT
.INDENT 0.0
.TP
.B \-t <FILENAME>, \-\-taxonomy\-dump=<FILENAME>
NCBI Taxonomy dump repository name
.UNINDENT
.INDENT 0.0
.TP
.B \-\-require\-rank=<RANK_NAME>
select sequence with taxid tag containing a parent of
rank <RANK_NAME>
.UNINDENT
.INDENT 0.0
.TP
.B \-r <TAXID>, \-\-required=<TAXID>
required taxid
.UNINDENT
.INDENT 0.0
.TP
.B \-i <TAXID>, \-\-ignore=<TAXID>
ignored taxid
.UNINDENT
.SH ECODBTAXSTAT USED SEQUENCE ATTRIBUTES
.INDENT 0.0
.INDENT 3.5
.INDENT 0.0
.IP \(bu 2
taxid
.UNINDENT
.UNINDENT
.UNINDENT
.SH AUTHOR
The OBITools Development Team - LECA
.SH COPYRIGHT
2019 - 2015, OBITool Development Team
.\" Generated by docutils manpage writer.
.