OpenMS
2.4.0
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Switches between different scores of peptide hits (PSMs) or protein hits in identification data.
In the idXML file format and in OpenMS' internal representation of identification data, every peptide spectrum match (PSM, "peptide hit") and every protein hit can be associated with a single numeric (quality) score of an arbitrary type. However, database search engines that generate PSMs or tools for post-processing of identification data may assign multiple scores of different types to each PSM/protein. These scores can be captured as meta data associated with the PSMs/proteins (in idXML: "UserParam" elements), but they are typically not considered by TOPP tools that utilize the scores. This utility allows to switch between "primary" scores and scores stored as meta values.
By default this tool operates on PSM scores; to consider protein scores instead, set the proteins
flag. The meta value that is supposed to replace the PSM/protein score - given by parameter new_score
- has to be numeric (type "float") and exist for every peptide or protein hit, respectively. The old score will be stored as a meta value, the name for which is given by the parameter old_score
. It is an error if a meta value with this name already exists for any hit, unless that meta value already stores the same score.
The command line parameters of this tool are:
IDScoreSwitcher -- Switches between different scores of peptide or protein hits in identification data 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: IDScoreSwitcher <options> Options (mandatory options marked with '*'): -in <file>* Input file (valid formats: 'idXML') -out <file>* Output file (valid formats: 'idXML') -new_score <name>* Name of the meta value to use as the new score -new_score_orientation <choice>* Orientation of the new score (are higher or lower values better?) (valid: 'lower_better', 'higher_better') -new_score_type <name> Name to use as the type of the new score (default: same as 'new_score') -old_score <name> Name to use for the meta value storing the old score (default: old score type) -proteins Apply to protein scores instead of PSM scores 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: