OpenMS
2.4.0
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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 Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06 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: