psm_utils
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compomics
Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
> A concrete use case this happens is with Mascot search results. For example, this mzIdentML snippet is from exporting results of a search against SwissProt: > > ``` >...
Hi there, I am using ms2resocre on my msgfplus resulted PSM files. I am using the following command to execute the ms2resocre `ms2rescore -p Desktop/Demo_data/data/20072102.mzid -s Desktop/Demo_data/data/20072102.mzML -c Desktop/Demo_data/config_file.json` I...
For example, `MSMSReader` fails to read the file if it has been encoded with a different encoding than the default one on the current machine...
Issues with newer PD MSF file versions have been reported. Check should check what is required to support newer versions of the file format.
Test coverage is currently reasonably low (38% at time of writing). Unit tests should be added and expanded for various parts of the code base. See Codecov for current coverage:...
WIth large mzid files it takes quite a lot of time to parse the source via the XML etree package. Removing this or parsing it another way can speedup mzid...
[edited after adding fix for PSM parsing] 1. As XTandem's protein names tend to be abbreviated in the protein "label" tag, change the origin to the "note" tag. 2. While...
