What does the argument -w and -t stand for?

[kimin0402]

Hi there,

I'm trying to compare mdust with sdust. For this purpose I found this program to be useful as I can download sdust as a stand alone copy. However, I'm having trouble understanding the parameter w and t. The default values for each parameters are 64 and 20 respectively, so I'm guessing w is supposed to be a cut-off value.

Is this right? Thank you in advance.

[peterjc]

This is essentially a limited functionality but faster rewrite of the NCBI DustMasker tool, and therefore the documentation for that is informative:

❯ dustmasker -help
USAGE
  dustmasker [-h] [-help] [-xmlhelp] [-in input_file_name]
    [-out output_file_name] [-window window_size] [-level level]
    [-linker linker] [-infmt input_format] [-outfmt output_format]
    [-parse_seqids] [-hard_masking] [-version-full] [-version-full-xml]
    [-version-full-json]

DESCRIPTION
   Low complexity region masker based on Symmetric DUST algorithm

OPTIONAL ARGUMENTS
 -h
   Print USAGE and DESCRIPTION;  ignore all other parameters
 -help
   Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
 -xmlhelp
   Print USAGE, DESCRIPTION and ARGUMENTS in XML format; ignore all other
   parameters
 -in <File_In>
   input file name
   Default = `-'
 -out <File_Out>
   output file name
   Default = `-'
 -window <Integer>
   DUST window length
   Default = `64'
 -level <Integer>
   DUST level (score threshold for subwindows)
   Default = `20'
 -linker <Integer>
   DUST linker (how close masked intervals should be to get merged together).
   Default = `1'
 -infmt <String>
   input format (possible values: fasta, blastdb)
   Default = `fasta'
 -outfmt <String, `acclist', `fasta', `interval', `maskinfo_asn1_bin',
                  `maskinfo_asn1_text', `maskinfo_xml', `seqloc_asn1_bin',
                  `seqloc_asn1_text', `seqloc_xml'>
   output format
   Default = `interval'
 -parse_seqids
   Parse Seq-ids in FASTA input
 -hard_masking
   Use hard masking for fasta outfmt
 -version-full
   Print extended version data;  ignore other arguments
 -version-full-xml
   Print extended version data in XML format;  ignore other arguments
 -version-full-json
   Print extended version data in JSON format;  ignore other arguments

Versus:

❯ sdust -h
Usage: sdust [-w 64] [-t 20] <in.fa>

Or:

❯ sdust -help
Usage: sdust [-w 64] [-t 20] <in.fa>

i.e. By analogy, sdust has -w rather than -window for "DUST window length" (default 64), and -t rather than -level for "DUST level (score threshold for subwindows)" (default 20).