mzid-filter

Filter MzIdentML according to a delimited text file and inject custom userParam entries into it.

Download:

Download the latest release link

Requirements:

• Java 8

Usage:

To print the usage info:
java -jar .\mzid-filter-X.X.jar without any parameters or with -h.

Typical usage example:
java -jar .\mzid-filter-X.X.jar --map "from-column-01" "to-userParam-01" --map "from-column-02" "to-userParam-02" --mzid <path-to.mzid> --psms <path-to-psm.tsv> --mapf <path-to-mappings-file>

Features:

• Mappings can be specified in a separate tab delimited file, one mapping per line. Specify the path to mappings file via --mapf option.
  An example of a mappings file can be found here.
  Mappings that are specified on the command line take precedence over the ones in the file.
• The delimiter in psm.tsv file is auto-detected (can be comma, tab, space or semicolon).
• The column in psm.tsv that is used for matching PSMs to mzid can be provided as a parameter via --psmidcol option. Defaults to Spectrum.
• By default --filter and --prune are both true.
  • --filter removes any PSMs from mzid that are not found in the PSMs file.
  • --prune also removes any unused information from mzid. Such as DBSequence entries, for example, which might not be referenced anymore after PSM removal by --filter.