'\" t
.\" Title: gt-cds
.\" Author: [FIXME: author] [see http://docbook.sf.net/el/author]
.\" Generator: DocBook XSL Stylesheets v1.79.1
.\" Date: 01/06/2017
.\" Manual: GenomeTools Manual
.\" Source: GenomeTools 1.5.9
.\" Language: English
.\"
.TH "GT\-CDS" "1" "01/06/2017" "GenomeTools 1\&.5\&.9" "GenomeTools Manual"
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.SH "NAME"
gt-cds \- Add CDS (coding sequence) features to exon features given in GFF3 file\&.
.SH "SYNOPSIS"
.sp
\fBgt cds\fR [option \&...] [GFF3_file]
.SH "DESCRIPTION"
.PP
\fB\-minorflen\fR [\fIvalue\fR]
.RS 4
set the minimum length an open reading frame (ORF) must have to be added as a CDS feature (measured in amino acids) (default: 64)
.RE
.PP
\fB\-startcodon\fR [\fIyes|no\fR]
.RS 4
require than an ORF must begin with a start codon (default: no)
.RE
.PP
\fB\-finalstopcodon\fR [\fIyes|no\fR]
.RS 4
require that the final ORF must end with a stop codon (default: no)
.RE
.PP
\fB\-seqfile\fR [\fIfilename\fR]
.RS 4
set the sequence file from which to take the sequences (default: undefined)
.RE
.PP
\fB\-encseq\fR [\fIfilename\fR]
.RS 4
set the encoded sequence indexname from which to take the sequences (default: undefined)
.RE
.PP
\fB\-seqfiles\fR
.RS 4
set the sequence files from which to extract the features use
\fI\-\-\fR
to terminate the list of sequence files
.RE
.PP
\fB\-matchdesc\fR [\fIyes|no\fR]
.RS 4
search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)
.RE
.PP
\fB\-matchdescstart\fR [\fIyes|no\fR]
.RS 4
exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace (default: no)
.RE
.PP
\fB\-usedesc\fR [\fIyes|no\fR]
.RS 4
use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries\&. If a description contains a sequence range (e\&.g\&., III:1000001\&.\&.2000000), the first part is used as sequence ID (\fIIII\fR) and the first range position as offset (\fI1000001\fR) (default: no)
.RE
.PP
\fB\-regionmapping\fR [\fIstring\fR]
.RS 4
set file containing sequence\-region to sequence file mapping (default: undefined)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-o\fR [\fIfilename\fR]
.RS 4
redirect output to specified file (default: undefined)
.RE
.PP
\fB\-gzip\fR [\fIyes|no\fR]
.RS 4
write gzip compressed output file (default: no)
.RE
.PP
\fB\-bzip2\fR [\fIyes|no\fR]
.RS 4
write bzip2 compressed output file (default: no)
.RE
.PP
\fB\-force\fR [\fIyes|no\fR]
.RS 4
force writing to output file (default: no)
.RE
.PP
\fB\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.sp
File format for option \fI\-regionmapping\fR:
.sp
The file supplied to option \-regionmapping defines a \(lqmapping\(rq\&. A mapping maps the sequence\-region entries given in the \fIGFF3_file\fR to a sequence file containing the corresponding sequence\&. Mappings can be defined in one of the following two forms:
.sp
.if n \{\
.RS 4
.\}
.nf
mapping = {
chr1 = "hs_ref_chr1\&.fa\&.gz",
chr2 = "hs_ref_chr2\&.fa\&.gz"
}
.fi
.if n \{\
.RE
.\}
.sp
or
.sp
.if n \{\
.RS 4
.\}
.nf
function mapping(sequence_region)
return "hs_ref_"\&.\&.sequence_region\&.\&."\&.fa\&.gz"
end
.fi
.if n \{\
.RE
.\}
.sp
The first form defines a Lua (http://www\&.lua\&.org) table named \(lqmapping\(rq which maps each sequence region to the corresponding sequence file\&. The second one defines a Lua function \(lqmapping\(rq, which has to return the sequence file name when it is called with the sequence_region as argument\&.
.SH "REPORTING BUGS"
.sp
Report bugs to \&.