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Created with Raphaël 2.2.016Nov13121110527Oct14969Sep824Jul20131130Jun2726242316151110985328May26221811643127Apr30Mar2322212019161312118613Feb1075427Jan26252423222120191817161514128765432131Dec26252322212013121110976543230Nov292322211918141130Oct292726181615131110965Adjusted hyperparams and processing architectureRemoved print functions that had been used for debuggingdebugged encoding processadjusted when cleave radius is supplied to produce flank encoding.fixed import error for other scripts in mhc_rank dirfixed bug in pssm retreival for flanking encodingadded feature to flank_encoding.py, enabling pssm scores to be added as first position in residue encoding vectorsextract cleavage site, converted pssm from pd.Series and pd.DataFrames to np.ndarrays, enabled pssm calculation.Added trim feature to seq_score of PSSM.py; Adjusted flanking_encoding.py to account for added encoding methods and for cleavage site extraction; Fixed bug in amino_acid.py so that correct encoding could be achievedCommented code for encodable_sequence.py processing alignment methodAdded alignment method to EncodableSequences class in encodable_sequences.py. Next commit will inlcude commentingAdded PSSM retrieval for peptides. Included padding functionality for peptides shorter than max length using PSSM of X at middle residues of max length k-mer. Also, fully commented code and added docstring for classFinalized / adjusted docstrings for all the methods of PSSM class. Still need to write docstrings for class itself.Added X PSSM scores to CSVs. Also, updated PSSM.py, specifically: added docstrings, commented code, introduced assertions to functions, and enabled pssm retreival for series of flank seqences from length 0 to 5Added MinMaxScaled blosum and physiochemical_blosum combo option for encodingMerge branch 'master' of https://code.osu.edu/skillman-lawrence.1/mhc_rankworking on encoding methods, specifically accomodating PSSM values for peptide and flanksRemoved files that did not pertain to peptide processingupdated amino acid encoding and created class to produce PSSM scoreedited amino_acid.pyDeleted Notebookss -> nameimproved-allele…improved-allele-parsinggot rid of extra echousing mhcgnomes instead of mhcnames to normalize allele names in sequence curationCurate phospho202010-phospho202010-phosphoupdateupdate iedb download urlupdate downloadsupdateAdd Solleder, ..., Gfeller Mol Cell Proteomics 2020 [PMID 31848261] to data_publishedbetter sequence alignmentMerge pull request #177 from openvax/202009-fixespre-2.1pre-2.1fixfixTweak fasta parsingUpdate README.mdTravis tweakv2.0.1v2.0.1A more future-proof tensorflow version dependencyVersion 2.0.1Fix typov2.0.0v2.0.0