NAME

       sak - Slicing and dicing of FASTA/FASTQ files..

SYNOPSIS

       sak [OPTIONS] [-o OUT.{fa,fq}] IN.{fa,fq}

DESCRIPTION

       "It slices, it dices and it makes the laundry!"

       Original SAK tool by David Weese. Rewrite by Manuel Holtgrewe.

REQUIRED ARGUMENTS

       IN INPUT_FILE
               Valid  filetypes  are:  .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*],
              .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam,  where  *
              is   any   of   the  following  extensions:  gz,  bz2,  and  bgzf  for  transparent
              (de)compression.

OPTIONS

       -h, --help
              Display the help message.

       --version
              Display version information.

   Output Options:
       -o, --out-path OUTPUT_FILE
              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, where *  is  any  of
              the following extensions: gz, bz2, and bgzf for transparent (de)compression.

       -rc, --revcomp
              Reverse-complement output.

       -l, --max-length INTEGER
              Maximal number of sequence characters to write out.

   Filter Options:
       -s, --sequence List of INTEGER's
              Select the given sequence for extraction by 0-based index.

       -sn, --sequence-name List of STRING's
              Select sequence with name prefix being NAME.

       -ss, --sequences List of STRING's
              Select sequences from-to where from and to are 0-based indices.

       -i, --infix List of STRING's
              Select characters from-to where from and to are 0-based indices.

       -ll, --line-length INTEGER
              Set  line  length  in  output  file.  See section Line Length for details. In range
              [-1..inf].

LINE LENGTH

       You can use the setting --line-length 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.

       The  default  is selected with a --line-length value of -1 and line breaks can be disabled
       with a value of 0.

USAGE EXAMPLES

       sak -s 10 IN.fa
              Cut out 11th sequence from IN.fa and write to stdout as FASTA.

       sak -ss 10-12 -ss 100-200 IN.fq
              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.