| OpenMS 2.5.0

DatabaseFilter

The DatabaseFilter tool filters a protein database in fasta format according to one or multiple filtering criteria.

The resulting database is written as output. Depending on the reporting method (method="whitelist" or "blacklist") only entries are retained that passed all filters ("whitelist) or failed at least one filter ("blacklist").

Implemented filter criteria:

accession: Filter database according to the set of protein accessions contained in an identification file (idXML, mzIdentML)

The command line parameters of this tool are:

    DatabaseFilter -- Filters a protein database (FASTA format) based on identified proteins

    Full documentation: http://www.openms.de/documentation/UTILS_DatabaseFilter.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    To cite OpenMS:

      Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

    Usage:

      DatabaseFilter <options>

    Options (mandatory options marked with '*'):

      -in <file>*        Input FASTA file, containing a database. (valid formats: 'fasta')

      -id <file>*        Input file containing identified peptides and proteins. (valid formats: 'idXML', 'mzid')

      -method <choice>   Switch between white-/blacklisting (default: 'whitelist' valid: 'whitelist', 'blacklist'

                         )

      -out <file>*       Output FASTA file where the reduced database will be written to. (valid formats: 'fasta'

                         )

    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
+DatabaseFilter Filters a protein database (FASTA format) based on identified proteins
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'DatabaseFilter'
in Input FASTA file, containing a database.input file*.fasta
id Input file containing identified peptides and proteins.input file*.idXML,*.mzid
method whitelist Switch between white-/blacklisting whitelist,blacklist
out Output FASTA file where the reduced database will be written to.output file*.fasta
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false