.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH SAK "1" "June 2017" "sak 2.3.1+dfsg-4" "User Commands"
.SH NAME
sak \- Slicing and dicing of FASTA/FASTQ files..
.PP
SYNOPSIS
.IP
sak [OPTIONS] [\-o OUT.{fa,fq}] IN.{fa,fq}
.PP
DESCRIPTION
.IP
"It slices, it dices and it makes the laundry!"
.IP
Original SAK tool by David Weese. Rewrite by Manuel Holtgrewe.
.PP
REQUIRED ARGUMENTS
.IP
IN INPUT_FILE
.IP
Valid filetypes are: .sam, .raw, .gbk, .frn, .fq, .fna, .ffn,
\&.fastq, .fasta, .faa, .fa, .embl, and .bam.
.PP
OPTIONS
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Display the help message.
.HP
\fB\-\-version\-check\fR BOOL
.IP
Turn this option off to disable version update notifications of the
application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO.
Default: 1.
.HP
\fB\-\-version\fR
.IP
Display version information.
.IP
Output Options:
.HP
\fB\-o\fR, \fB\-\-out\-path\fR OUTPUT_FILE
.IP
Path to the resulting file. If omitted, result is printed to stdout
in FastQ format. Valid filetypes are: .sam, .raw, .frn, .fq, .fna,
\&.ffn, .fastq, .fasta, .faa, .fa, and .bam.
.HP
\fB\-rc\fR, \fB\-\-revcomp\fR
.IP
Reverse\-complement output.
.HP
\fB\-l\fR, \fB\-\-max\-length\fR INTEGER
.IP
Maximal number of sequence characters to write out.
.IP
Filter Options:
.HP
\fB\-s\fR, \fB\-\-sequence\fR List of INTEGER's
.IP
Select the given sequence for extraction by 0\-based index.
.HP
\fB\-sn\fR, \fB\-\-sequence\-name\fR List of STRING's
.IP
Select sequence with name prefix being NAME.
.HP
\fB\-ss\fR, \fB\-\-sequences\fR List of STRING's
.IP
Select sequences from\-to where from and to are 0\-based indices.
.HP
\fB\-i\fR, \fB\-\-infix\fR List of STRING's
.IP
Select characters from\-to where from and to are 0\-based indices.
.HP
\fB\-ll\fR, \fB\-\-line\-length\fR INTEGER
.IP
Set line length in output file. See section Line Length for details.
In range [\-1..inf].
.PP
LINE LENGTH
.IP
You can use the setting \fB\-\-line\-length\fR for setting the resulting line
length. By default, sequences in FASTA files are written with at most 70
characters per line and sequences in FASTQ files are written without any
line breaks. The quality sequence in FASTQ file is written in the same way
as the residue sequence.
.IP
The default is selected with a \fB\-\-line\-length\fR value of \fB\-1\fR and line breaks
can be disabled with a value of 0.
.PP
USAGE EXAMPLES
.IP
sak \fB\-s\fR 10 IN.fa
.IP
Cut out 11th sequence from IN.fa and write to stdout as FASTA.
.IP
sak \fB\-ss\fR 10\-12 \fB\-ss\fR 100\-200 IN.fq
.IP
Cut out 11th up to and including 12th and 101th up to and including
199th sequence from IN.fq and write to stdout as FASTA.
.PP
VERSION
.IP
Last update:
sak version: 0.4.6 [tarball]
SeqAn version: 2.3.1