.\" Man page generated from reStructuredText.
.
.TH "OBISILVA" "1" "Jan 28, 2019" " 1.02 12" "OBITools"
.SH NAME
obisilva \- description of obisilva
.
.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
\fI\%obisilva\fP: converts and optionally download the \fI\%Silva database\fP
into an ecoPCR database. The formated database include the taxonomy as defined by the Silva authors.
.sp
\fBWARNING:\fP
.INDENT 0.0
.INDENT 3.5
Take care that the numeric taxids associated to the sequences are specific 
to this Silva database and not compatible with the NCBI taxids. 
The taxids present in a version of the Silva database (\fIi.e\fP ssu, lsu, parc, ref…)
are are just valid for this version of the database and not compatible 
with the taxids used in another version.
.UNINDENT
.UNINDENT
.SH OBISILVA SPECIFIC OPTIONS
.INDENT 0.0
.TP
.B \-s, \-\-ssu
.INDENT 7.0
.INDENT 3.5
Specify that you are interested in the \fBSSU\fP database.
.UNINDENT
.UNINDENT
.sp
\fIExample:\fP
.INDENT 7.0
.INDENT 3.5
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
> obisilva \-\-ssu \-\-parc
.ft P
.fi
.UNINDENT
.UNINDENT
.sp
This download and format into an ecoPCR database the latest version of the \fBSSUParc\fP database of \fBSilva\fP\&.
.UNINDENT
.UNINDENT
.UNINDENT
.INDENT 0.0
.TP
.B \-l, \-\-lsu
.INDENT 7.0
.INDENT 3.5
Specify that you are interested in the \fBLSU\fP database.
.UNINDENT
.UNINDENT
.sp
\fIExample:\fP
.INDENT 7.0
.INDENT 3.5
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
> obisilva \-\-ssu \-\-parc
.ft P
.fi
.UNINDENT
.UNINDENT
.sp
This download and format into an ecoPCR database the latest version of the \fBLSUParc\fP database of \fBSilva\fP\&.
.UNINDENT
.UNINDENT
.UNINDENT
.INDENT 0.0
.TP
.B \-p, \-\-parc
Specify that you are interested in the \fBParc\fP (complete) version of the \fBSilva\fP database.
.UNINDENT
.INDENT 0.0
.TP
.B \-r, \-\-ref
Specify that you are interested in the \fBReference\fP (cleaned to keep only high quality sequences)
version of the \fBSilva\fP database.
.UNINDENT
.INDENT 0.0
.TP
.B \-n, \-\-nr
Specify that you are interested in the \fBNon redundant\fP version of the \fBSilva\fP database.
just a version of the to closely related sequence is kept in this version of the database
.sp
\fBWARNING:\fP
.INDENT 7.0
.INDENT 3.5
Non redundant version of \fBSilva\fP exists only for the SSU sequences
in its \fBReference\fP and  \fBTruncated\fP version
.UNINDENT
.UNINDENT
.UNINDENT
.INDENT 0.0
.TP
.B \-t, \-\-trunc
Specify that you are interested in the \fBTruncated\fP (limited to the rDNA element without flanked regions)
version of the \fBSilva\fP database.
.UNINDENT
.INDENT 0.0
.TP
.B \-\-local=<DIRNAME>
.INDENT 7.0
.INDENT 3.5
Specify you have already downloaded a copy of the \fBSilva\fP database located at the following URL
\fI\%http://www.arb\-**Silva**.de/no_cache/download/archive/current/Exports/\fP
.UNINDENT
.UNINDENT
.sp
\fIExample:\fP
.INDENT 7.0
.INDENT 3.5
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
> obisilva \-\-ssu \-\-parc \-\-local=**Silva**Dir
.ft P
.fi
.UNINDENT
.UNINDENT
.sp
This format the \fBSSUParc\fP version of the \fBSilva\fP database pre\-downloaded in the \fI**Silva**Dir\fP directory.
.UNINDENT
.UNINDENT
.UNINDENT
.SH COMMON OPTIONS
.INDENT 0.0
.TP
.B \-h, \-\-help
Shows this help message and exits.
.UNINDENT
.INDENT 0.0
.TP
.B \-\-DEBUG
Sets logging in debug mode.
.UNINDENT
.SH AUTHOR
The OBITools Development Team - LECA
.SH COPYRIGHT
2019 - 2015, OBITool Development Team
.\" Generated by docutils manpage writer.
.