.\" Man page generated from reStructuredText.
.
.TH "OBICOMPLEMENT" "1" "Jul 27, 2019" " 1.02 13" "OBITools"
.SH NAME
obicomplement \- description of obicomplement
.
.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\%obicomplement\fP reverse\-complements the sequence records.
.INDENT 0.0
.INDENT 3.5
.sp
\fBTIP:\fP
.INDENT 0.0
.INDENT 3.5
The identifiers of the sequence records are modified by appending
to them the \fB_CMP\fP suffix.
.UNINDENT
.UNINDENT
.sp
\fBTIP:\fP
.INDENT 0.0
.INDENT 3.5
a attribute with key \fBcomplemented\fP and value sets to \fBTrue\fP is added
on each reversed complemented sequence record.
.UNINDENT
.UNINDENT
.UNINDENT
.UNINDENT
.sp
By using the selection option set, it is possible to reverse complement only a subset of the
sequence records included in the input file. The selected sequence are reversed complemented,
others are stored without modification
.INDENT 0.0
.INDENT 3.5
\fIExample 1:\fP
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
> obicomplement seq.fasta > seqRC.fasta
.ft P
.fi
.UNINDENT
.UNINDENT
.sp
Reverses complements all sequence records from the \fBseq.fasta\fP file and stores the 
result to the \fBseqRC.fasta\fP file.
.sp
\fIExample 2:\fP
.INDENT 0.0
.INDENT 3.5
.sp
.nf
.ft C
> obicomplement \-s \(aqA{10,}$\(aq seq.fasta > seqRC.fasta
.ft P
.fi
.UNINDENT
.UNINDENT
.sp
Reverses complements sequence records from the \fBseq.fasta\fP file only if they finish
by at least 10 \fBA\fP\&. Others sequences are stored without modification.
.UNINDENT
.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 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.
.