1SAK(1)                                                                  SAK(1)
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NAME

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

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

12       "It slices, it dices and it makes the laundry!"
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14       Original SAK tool by David Weese. Rewrite by Manuel Holtgrewe.
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REQUIRED ARGUMENTS

17       IN INPUT_FILE
18               Valid  filetypes  are: .sam, .raw, .gbk, .frn, .fq, .fna, .ffn,
19              .fastq, .fasta, .faa, .fa, and .embl.
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OPTIONS

22       -h, --help
23              Display the help message.
24
25       --version
26              Display version information.
27
28   Output Options:
29       -o, --out-path OUTPUT_FILE
30              Path to the resulting file.  If omitted, result  is  printed  to
31              stdout  in  FastQ format. Valid filetypes are: .sam, .raw, .frn,
32              .fq, .fna, .ffn, .fastq, .fasta, .faa, and .fa.
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34       -rc, --revcomp
35              Reverse-complement output.
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37       -l, --max-length INTEGER
38              Maximal number of sequence characters to write out.
39
40   Filter Options:
41       -s, --sequence List of INTEGER's
42              Select the given sequence for extraction by 0-based index.
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44       -sn, --sequence-name List of STRING's
45              Select sequence with name prefix being NAME.
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47       -ss, --sequences List of STRING's
48              Select sequences from-to where from and to are 0-based indices.
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50       -i, --infix List of STRING's
51              Select characters from-to where from and to are 0-based indices.
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53       -ll, --line-length INTEGER
54              Set line length in output file.  See  section  Line  Length  for
55              details. In range [-1..inf].
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LINE LENGTH

58       You  can  use  the setting --line-length for setting the resulting line
59       length.  By default, sequences in FASTA files are written with at  most
60       70 characters per line and sequences in FASTQ files are written without
61       any line breaks.  The quality sequence in FASTQ file is written in  the
62       same way as the residue sequence.
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64       The  default  is  selected  with  a  --line-length value of -1 and line
65       breaks can be disabled with a value of 0.
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USAGE EXAMPLES

68       sak -s 10 IN.fa
69              Cut out 11th sequence from IN.fa and write to stdout as FASTA.
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71       sak -ss 10-12 -ss 100-200 IN.fq
72              Cut out 11th up to and  including  12th  and  101th  up  to  and
73              including  199th  sequence  from  IN.fq  and  write to stdout as
74              FASTA.
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78sak 0.4.8 [tarball]                                                     SAK(1)
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