Parallel Identification Reading and Relaxed file naming in input psms list

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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Parallel Identification Reading and Relaxed file naming in input psms list #115

Closed trishorts closed 2 years ago

trishorts commented 2 years ago

Input processing is not currently parallel. IDs are read line by line and processed individually. This PR reads all the input lines, breaks them into groups by file, then processes all the ids in that file before adding them to the group.

In this PR, we also allow flexibility in filenames for the psms input file. The filename can be with or without extension and can have or have not a full file path. also windows and linux filepaths are explicitly tested.

Alexander-Sol commented 2 years ago

Test coverage looks good, but I don't have a linux machine to be absolutely sure.