'\" t
.\"     Title: gt-seq
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 02/28/2024
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.5
.\"  Language: English
.\"
.TH "GT\-SEQ" "1" "02/28/2024" "GenomeTools 1\&.6\&.5" "GenomeTools Manual"
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.SH "NAME"
gt-seq \- Parse the given sequence file(s) and construct the corresponding index files\&.
.SH "SYNOPSIS"
.sp
\fBgt seq\fR [option \&...] sequence_file [\&...]
.SH "DESCRIPTION"
.PP
\fB\-recreate\fR [\fIyes|no\fR]
.RS 4
recreate index files, even if they exist already (default: no)
.RE
.PP
\fB\-showfasta\fR [\fIyes|no\fR]
.RS 4
show all sequences (in FASTA format) (default: no)
.RE
.PP
\fB\-showseqnum\fR [\fIvalue\fR]
.RS 4
show sequence with given number (sequences are counted from 1 unless \-seqnum_from_0 is specified) (default: undefined)
.RE
.PP
\fB\-showseqlength\fR [\fIvalue\fR]
.RS 4
show length of sequence with given number (sequences are counted from 1 unless \-seqnum_from_0 is specified) (default: undefined)
.RE
.PP
\fB\-showseqnum_inputfile\fR [\fIfilename\fR]
.RS 4
show sequence with given numbers specified line by line in given file (sequences are counted from 1 unless \-seqnum_from_0 is specified) (default: undefined)
.RE
.PP
\fB\-seqnum_from_0\fR [\fIyes|no\fR]
.RS 4
for options \-showseqnum and \-showseqnum_inputfile: count sequence numbers from 0 instead of 1 (default: no)
.RE
.PP
\fB\-gc\-content\fR [\fIyes|no\fR]
.RS 4
print GC\-content (for DNA files) (default: no)
.RE
.PP
\fB\-stat\fR [\fIyes|no\fR]
.RS 4
show sequence statistics (default: no)
.RE
.PP
\fB\-seqlengthdistri\fR [\fIyes|no\fR]
.RS 4
show sequence length distribution (default: no)
.RE
.PP
\fB\-width\fR [\fIvalue\fR]
.RS 4
set output width for FASTA sequence printing (0 disables formatting) (default: 0)
.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
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.