psm-convert

Usage:

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

Description:

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

Input:

• input PSM file – The name of a PSM file in tab-delimited text, SQT, pepXML or mzIdentML format
• output format – The desired format of the output file. Legal values are tsv, html, sqt, pin, pepxml, mzidentml.

Output:

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

• psm-convert.log.txt – a log file containing a copy of all messages that were printed to stderr.
• psm-convert.params.txt – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.

Options:

• psm-convert options

  • --input-format auto|tsv|sqt|pepxml|mzidentml – Legal values are auto, tsv, sqt, pepxml or mzidentml format. Default = auto.
  • --distinct-matches T|F – Whether matches/ion are distinct (as opposed to total). Default = true.
  • --protein-database <string> – The name of the file in FASTA format. Default = <empty>.

• Input and output

  • --output-dir <string> – The name of the directory where output files will be created. Default = crux-output.
  • --overwrite T|F – Replace existing files if true or fail when trying to overwrite a file if false. Default = false.
  • --parameter-file <string> – A file containing parameters. See the parameter documentation page for details. Default = <empty>.
  • --verbosity <integer> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = 30.