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

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

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

       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.

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

-h, --help
              Display the help message.

       --version
              Display version information.

   OutputOptions:-o, --out-pathOUTPUT_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-lengthINTEGER
              Maximal number of sequence characters to write out.

   FilterOptions:-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-lengthINTEGER
              Set line length in output file.  See section LineLength for details. In range [-1..inf].

ININPUT_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.

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

sak-s10IN.fa
              Cut out 11th sequence from IN.fa and write to stdout as FASTA.

       sak-ss10-12-ss100-200IN.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.

sak 0.4.8 [tarball]                                                                                       SAK(1)