update README and fix validation

README.md

@@ -3,4 +3,48 @@
 ![Build](https://github.com/meyer-lab/resistance-MS/workflows/Build/badge.svg)
 ![Test](https://github.com/meyer-lab/resistance-MS/workflows/Test/badge.svg)
 
-Predicting cell phenotype with mass spec data.
+Clusters peptides based on both sequence similarity and phosphorylation signal across samples.
+
+
+## Usage
+
+```
+>>> from ddmc.clustering import DDMC
+
+>>> # load dataset as p_signal...
+
+>>> p_signal
+             Sample 1  Sample 2  Sample 3  Sample 4  Sample 5
+Sequence                                                     
+AAAAAsQQGSA -3.583614       NaN -0.662659 -1.320029 -0.730832
+AAAAGsASPRS -0.174779 -1.796899  0.891798 -3.092941  2.394315
+AAAAGsGPSPP -1.951552 -2.937095  2.692876 -2.344894  0.556615
+AAAAGsGPsPP  3.666782       NaN -2.081231  0.989394       NaN
+AAAAPsPGSAR  1.753855 -2.135835  0.896778  3.369230  2.020967
+...               ...       ...       ...       ...       ...
+YYSPYsVSGSG -3.502871  2.831169  3.383486  2.589559  3.624968
+YYSSRsQSGGY -0.870365  0.887317  2.600291 -0.374107  3.285459
+YYTAGyNSPVK  0.249539  2.047050 -0.286033  0.042650  2.863317
+YYTSAsGDEMV  0.662787  0.135326 -1.004350  0.879398 -1.609894
+YYYSSsEDEDS       NaN -1.101679 -3.273987 -0.872370 -1.735891
+
+>>> p_signal.index  # p_signal.index contains the peptide sequences
+Index(['AAAAAsQQGSA', 'AAAAGsASPRS', 'AAAAGsGPSPP', 'AAAAGsGPsPP',
+       'AAAAPsPGSAR', 'AAAAPsPGsAR', 'AAAARsLLNHT', 'AAAARsPDRNL',
+       'AAAARtQAPPT', 'AAADFsDEDED',
+       ...
+       'YYDRMySYPAR', 'YYEDDsEGEDI', 'YYGGGsEGGRA', 'YYRNNsFTAPS',
+       'YYSPDyGLPSP', 'YYSPYsVSGSG', 'YYSSRsQSGGY', 'YYTAGyNSPVK',
+       'YYTSAsGDEMV', 'YYYSSsEDEDS'],
+      dtype='object', name='Sequence', length=30561)
+      
+>>> model = DDMC(n_components=2, seq_weight=100).fit(p_signal)  # fit model
+
+>>> model.transform(as_df=True)  # get cluster centers
+                 0         1
+Sample 1  0.017644  0.370375
+Sample 2 -0.003625 -0.914869
+Sample 3 -0.087624 -0.682140
+Sample 4  0.014644 -0.658907
+Sample 5  0.023885  0.196063
+```

ddmc/clustering.py

@@ -98,7 +98,7 @@ def fit(self, p_signal: pd.DataFrame):
             isinstance(sequences[0], str) and len(sequences[0]) == 11
         ), "The index of p_signal must be the peptide sequences of length 11"
         assert all(
-            [token in AAlist for token in sequences[0]]
+            [token.upper() in AAlist for token in sequences[0]]
         ), "Sequence(s) contain invalid characters"
         assert (
             p_signal.select_dtypes(include=[np.number]).shape[1] == p_signal.shape[1]