.\" Man page generated from reStructuredText.
.
.TH "OBICONVERT" "1" "Jul 27, 2019" " 1.02 13" "OBITools"
.SH NAME
obiconvert \- description of obiconvert
.
.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\%obiconvert\fP converts sequence files to different output formats.
See the documentation for more details on the different formats.
.sp
Input files can be in :
.INDENT 0.0
.INDENT 3.5
.INDENT 0.0
.IP \(bu 2
\fIfasta\fP format
.IP \(bu 2
\fIextended OBITools fasta\fP format
.IP \(bu 2
Sanger \fIfastq\fP format
.IP \(bu 2
Solexa \fIfastq\fP format
.IP \(bu 2
\fIecoPCR\fP format
.IP \(bu 2
\fIecoPCR\fP database format
.IP \(bu 2
\fIGenBank\fP format
.IP \(bu 2
\fIEMBL\fP format
.UNINDENT
.UNINDENT
.UNINDENT
.sp
\fI\%obiconvert\fP converts those files to the :
.INDENT 0.0
.INDENT 3.5
.INDENT 0.0
.IP \(bu 2
\fIextended OBITools fasta\fP format
.IP \(bu 2
Sanger \fIfastq\fP format
.IP \(bu 2
\fIecoPCR\fP database format
.UNINDENT
.UNINDENT
.UNINDENT
.sp
If no file name is specified, data is read from standard input.
.sp
\fIExamples:\fP
.INDENT 0.0
.INDENT 3.5
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
> obiconvert \-\-ecopcrdb \-\-fasta\-output \e
  \(aqmy_ecopcr_database\(aq > sequences.fasta
.ft P
.fi
.UNINDENT
.UNINDENT
.sp
Converts an ecoPCR database in a sequence file in \fIextended OBITools fasta\fP format.
.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
.SH OPTIONS TO SPECIFY INPUT FORMAT
.SS Restrict the analysis to a sub\-part of the input file
.INDENT 0.0
.TP
.B \-\-skip <N>
The N first sequence records of the file are discarded from the analysis and
not reported to the output file
.UNINDENT
.INDENT 0.0
.TP
.B \-\-only <N>
Only the N next sequence records of the file are analyzed. The following sequences
in the file are neither analyzed, neither reported to the output file.
This option can be used conjointly with the \fI–skip\fP option.
.UNINDENT
.SS Sequence annotated format
.INDENT 0.0
.TP
.B \-\-genbank
Input file is in genbank format.
.UNINDENT
.INDENT 0.0
.TP
.B \-\-embl
Input file is in embl format.
.UNINDENT
.SS fasta related format
.INDENT 0.0
.TP
.B \-\-fasta
Input file is in fasta format (including
OBITools fasta extensions).
.UNINDENT
.SS fastq related format
.INDENT 0.0
.TP
.B \-\-sanger
Input file is in Sanger fastq format (standard
fastq used by HiSeq/MiSeq sequencers).
.UNINDENT
.INDENT 0.0
.TP
.B \-\-solexa
Input file is in fastq format produced by
Solexa (Ga IIx) sequencers.
.UNINDENT
.SS ecoPCR related format
.INDENT 0.0
.TP
.B \-\-ecopcr
Input file is in ecoPCR format.
.UNINDENT
.INDENT 0.0
.TP
.B \-\-ecopcrdb
Input is an ecoPCR database.
.UNINDENT
.SS Specifying the sequence type
.INDENT 0.0
.TP
.B \-\-nuc
Input file contains nucleic sequences.
.UNINDENT
.INDENT 0.0
.TP
.B \-\-prot
Input file contains protein sequences.
.UNINDENT
.SH OPTIONS TO SPECIFY OUTPUT FORMAT
.SS Standard output format
.INDENT 0.0
.TP
.B \-\-fasta\-output
Output sequences in \fBOBITools\fP fasta format
.UNINDENT
.INDENT 0.0
.TP
.B \-\-fastq\-output
Output sequences in Sanger fastq format
.UNINDENT
.SS Generating an ecoPCR database
.INDENT 0.0
.TP
.B \-\-ecopcrdb\-output=<PREFIX_FILENAME>
Creates an ecoPCR database from sequence records results
.UNINDENT
.SS Miscellaneous option
.INDENT 0.0
.TP
.B \-\-uppercase
Print sequences in upper case (default is lower case)
.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.
.