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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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Allow any string as protein name #111

Closed trishorts closed 2 years ago

trishorts commented 2 years ago

in https://github.com/smith-chem-wisc/FlashLFQ/issues/103 wsnoble requests that we allow any unique string to be used as a protein name. percolator cannot control how users format the strings in that column. this pr eliminates the former behavior of parsing protein accession and gene from a fasta like header and just taking them as is.

rmillikin commented 2 years ago

should be able to do this simply by changing delimiters in Util.PsmReader.cs https://github.com/smith-chem-wisc/FlashLFQ/blob/3bd724b3b64ca6889e542e151d54d2f54e4e7cec/Util/PsmReader.cs#L38

change: { PsmFileType.Percolator, new string[] { "|", "," } }, to: { PsmFileType.Percolator, new string[] { "," } },

i.e., just remove "|" from the Percolator delimiters