crux psm-convert

Usage:

crux psm-convert [options] <input PSM file> <output format>

Description:

This command reads in a file containing peptide-spectrum matches (PSMs) in one of a variety of supported formats and outputs the same PSMs in a different format.

Input:

Output:

The program writes the following files to the folder crux-output. The name of the output folder can be set by the user using the --output-dir option.

Options:


Implementation suggestions:

  1. Subclass CruxApplication to create a PSMConvertApplication class.
  2. Looking at MzIdentMLWriter, PMCPepXMLWriter, PepXMLWriter, SQTWriter, and MatchFileWriter, etc., derive an abstract class "PSMWriter" with virtual methods for writing out a MatchCollection or ProteinMatchCollection. Make all writers a subclass of this abstract class. You will need to standardize the abstract method calls over all of the writers e.g. virtual writePSM(Match*), writeCollection(MatchCollection*), etc.
  3. Similiar to step #2, look at the MzIdentMLReader, PepXMLReader, SQTReader, and MatchFileReader class and derive an abstract class "PSMReader" that returns a MatchCollection or ProteinMatchCollection after parsing the inputed data file.
  4. Implement PSMConvertApplication, that parses the (<input PSM file>) using the correct file format parser (either determined by file extension or --input-format parameter) and then write out the psms in the (<output format>)

Notes:


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