.TH SAK 1 "" "sak 0.4.8 [tarball]" ""
.SH NAME
sak \- Slicing and dicing of FASTA/FASTQ files..
.SH SYNOPSIS
\fBsak\fP [\fIOPTIONS\fP] [\fB-o\fP \fIOUT.{fa,fq}\fP] \fIIN.{fa,fq}\fP
.SH DESCRIPTION
"It slices, it dices and it makes the laundry!"
.sp
Original SAK tool by David Weese. Rewrite by Manuel Holtgrewe.
.SH REQUIRED ARGUMENTS
.TP
\fBIN\fP \fIINPUT_FILE\fP
 Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.gbk[.*]\fP, \fI.frn[.*]\fP, \fI.fq[.*]\fP, \fI.fna[.*]\fP, \fI.ffn[.*]\fP, \fI.fastq[.*]\fP, \fI.fasta[.*]\fP, \fI.faa[.*]\fP, \fI.fa[.*]\fP, \fI.embl[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.SH OPTIONS
.TP
\fB-h\fP, \fB--help\fP
Display the help message.
.TP
\fB--version\fP
Display version information.
.SS Output Options:
.TP
\fB-o\fP, \fB--out-path\fP \fIOUTPUT_FILE\fP
Path to the resulting file.  If omitted, result is printed to stdout in FastQ format. Valid filetypes are: \fI.sam[.*]\fP, \fI.raw[.*]\fP, \fI.frn[.*]\fP, \fI.fq[.*]\fP, \fI.fna[.*]\fP, \fI.ffn[.*]\fP, \fI.fastq[.*]\fP, \fI.fasta[.*]\fP, \fI.faa[.*]\fP, \fI.fa[.*]\fP, and \fI.bam\fP, where * is any of the following extensions: \fIgz\fP, \fIbz2\fP, and \fIbgzf\fP for transparent (de)compression.
.TP
\fB-rc\fP, \fB--revcomp\fP
Reverse-complement output.
.TP
\fB-l\fP, \fB--max-length\fP \fIINTEGER\fP
Maximal number of sequence characters to write out.
.SS Filter Options:
.TP
\fB-s\fP, \fB--sequence\fP List of \fIINTEGER\fP's
Select the given sequence for extraction by 0-based index.
.TP
\fB-sn\fP, \fB--sequence-name\fP List of \fISTRING\fP's
Select sequence with name prefix being \fINAME\fP.
.TP
\fB-ss\fP, \fB--sequences\fP List of \fISTRING\fP's
Select sequences \fIfrom\fP-\fIto\fP where \fIfrom\fP and \fIto\fP are 0-based indices.
.TP
\fB-i\fP, \fB--infix\fP List of \fISTRING\fP's
Select characters \fIfrom\fP-\fIto\fP where \fIfrom\fP and \fIto\fP are 0-based indices.
.TP
\fB-ll\fP, \fB--line-length\fP \fIINTEGER\fP
Set line length in output file.  See section \fILine Length\fP for details. In range [-1..inf].
.SH LINE LENGTH
You can use the setting \fB--line-length\fP 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.
.sp
The default is selected with a \fB--line-length\fP value of \fI-1\fP and line breaks can be disabled with a value of \fI0\fP.
.SH USAGE EXAMPLES
.TP
\fBsak\fP \fB-s\fP \fI10\fP \fIIN.fa\fP
Cut out 11th sequence from \fIIN.fa\fP and write to stdout as FASTA.
.TP
\fBsak\fP \fB-ss\fP \fI10-12\fP \fB-ss\fP \fI100-200\fP \fIIN.fq\fP
Cut out 11th up to and including 12th and 101th up to and including 199th sequence from \fIIN.fq\fP and write to stdout as FASTA.