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Digestor

Digests a protein database in-silico.

pot. predecessor tools $ \longrightarrow $ Digestor $ \longrightarrow $ pot. successor tools
none (FASTA input) IDFilter (peptide blacklist)

This application is used to digest a protein database to get all peptides given a cleavage enzyme. At the moment only trypsin is supported.

The output can be used as a blacklist filter input to IDFilter, to remove certain peptides.

Note
For mzid in-/out- put, due to legacy reason issues you are temporarily asked to use IDFileConverter as a wrapper. The command line parameters of this tool are:
Digestor -- Digests a protein database in-silico.
Version: 2.0.0 Aug 19 2015, 22:19:33, Revision: GIT-NOTFOUND

Usage:
  Digestor <options>

Options (mandatory options marked with '*'):
  -in <file>*                 Input file (valid formats: 'fasta')
  -out <file>*                Output file (peptides) (valid formats: 'idXML', 'fasta')
  -out_type <type>            Set this if you cannot control the filename of 'out', e.g., in TOPPAS. (valid: 
                              'idXML', 'fasta')
  -missed_cleavages <number>  The number of allowed missed cleavages (default: '1' min: '0')
  -min_length <number>        Minimum length of peptide (default: '6')
  -max_length <number>        Maximum length of peptide (default: '40')
  -enzyme <string>            The type of digestion enzyme (default: 'Trypsin' valid: 'Trypsin', 'none')
                              
Common UTIL options:
  -ini <file>                 Use the given TOPP INI file
  -threads <n>                Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini <file>           Writes the default configuration file
  --help                      Shows options
  --helphelp                  Shows all options (including advanced)

INI file documentation of this tool:
Legend:
required parameter
advanced parameter
+DigestorDigests a protein database in-silico.
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'Digestor'
in input fileinput file*.fasta
out Output file (peptides)output file*.idXML,*.fasta
out_type Set this if you cannot control the filename of 'out', e.g., in TOPPAS.idXML,fasta
missed_cleavages1 The number of allowed missed cleavages0:∞
min_length6 Minimum length of peptide
max_length40 Maximum length of peptide
enzymeTrypsin The type of digestion enzymeTrypsin,none
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue,false
forcefalse Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:32 using doxygen 1.8.9.1