Merges multiple .mzid files created by MS-GF+ into a single mzid file.
This is primarily designed for "split-fasta" MS-GF+ searches, where a large protein database was split into multiple .fasta files, and then each one used to search a single spectra file.
MzidMerger reads in the mzids from MS-GF+ and creates a new mzid file using the contents of the input mzid files
MzidMerger uses PSI_Interface.dll for reading and writing the mzids.
MzidMerger -inDir "directory path" [-filter "filename filter"] [-out "output file path"] [-maxSpecEValue number] [-keepOnlyBestResults] [-fixIds]
-inDir path
- Path to directory containing mzid files to be merged. If the path has spaces, it must be in quotes.
-filter:abc*.mzid
- Filename filter; filenames that match this string will be merged. *.mzid and .mzid.gz are appended if neither ends the filter string. Use '' for wildcard matches. (Default: All files ending in .mzid or .mzid.gz).
-out
- Filepath/filename of output file; if no path, input directory is used; by default will determine and use the common portion of the input file names.
-maxSpecEValue
- Maximum SpecEValue to include in the merged file. Default value includes all results.
-keepOnlyBestResults
- If specified, only the best-scoring results for each spectrum are kept.
-fixIds
- Fix the peptide and peptideEvidence IDs. Only use for e.g. older MS-GF+ results, that output many errors about duplicate IDs. Only fixes Peptide and PeptideEvidence IDs.
Written by Bryson Gibbons and Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
E-mail: proteomics@pnnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://panomics.pnnl.gov/ or https://www.pnnl.gov/integrative-omics
The MzidMerger is licensed under the 2-Clause BSD License; you may not use this file except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause
Copyright 2018 Battelle Memorial Institute