percolator output compatibilty

smith-chem-wisc / FlashLFQ

Ultra-fast label-free quantification algorithm for mass-spectrometry proteomics

GNU Lesser General Public License v3.0

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percolator output compatibilty #104

Closed trishorts closed 2 years ago

trishorts commented 2 years ago

There was a request by Noble lab to add support for percolator output. For legacy percolator output, there are three issues: no filename is supplied, no retention time is supplied, and protein groups info is a list of truncated fasta headers. This PR deals with the last two problems. Users must include the filename. This PR recovers the RT from the raw file and this PR determines the protein groups.

https://github.com/smith-chem-wisc/FlashLFQ/issues/103

acesnik commented 2 years ago

It looks like there's an issue with a test

trishorts commented 2 years ago

apologies for the hic-ups. should be ready at least for a preliminary review