Protein function prediction with GO - Part 3

chebai/preprocessing/bin/protein_token/tokens.txt

@@ -18,3 +18,4 @@ W
 E
 V
 H
+X

chebai/preprocessing/bin/protein_token_3_gram/tokens.txt

@@ -7998,3 +7998,362 @@ WWC
 WCC
 WCH
 WWM
+TAX
+AXD
+XDR
+IEX
+EXV
+QAX
+AXX
+XXE
+XES
+MXN
+XNF
+NRX
+RXX
+XXX
+XXR
+XRI
+SAX
+AXG
+XGG
+PRX
+RXR
+XRX
+RXE
+XEF
+QEX
+EXQ
+XQR
+REX
+EXR
+RXQ
+XQQ
+DRX
+RXP
+XPG
+QMX
+MXT
+XTX
+TXR
+XRM
+APX
+PXX
+XXG
+XGI
+NLX
+LXX
+XXM
+XMA
+LNX
+NXE
+XEA
+GTX
+TXN
+XND
+LIX
+IXI
+XIM
+MVX
+VXX
+XXK
+XKT
+GLX
+LXP
+XPP
+QGX
+GXD
+XDL
+XAP
+QNX
+NXM
+XMN
+VAX
+XGV
+IKX
+KXY
+KEX
+EXL
+XLY
+GQX
+QXE
+XEP
+PLX
+XKC
+PVX
+XKE
+RXI
+XIR
+AXL
+XLN
+LLX
+LXD
+XDA
+AXE
+XEL
+GGX
+GXG
+KAX
+XXA
+XAG
+XWS
+SPX
+PXC
+XCD
+GWX
+WXH
+XHF
+MPX
+ESX
+SXN
+XNK
+DLX
+LXN
+XNS
+QXG
+XGD
+ITX
+XRG
+NEX
+EXA
+XAL
+LDX
+DXI
+XII
+TPX
+PXM
+XMR
+NXG
+XGY
+ASX
+SXV
+XVE
+TKX
+KXA
+KRX
+XXT
+XTL
+IDX
+DXX
+XXL
+XLV
+AKX
+KXX
+QHX
+HXV
+XVN
+NSX
+SXX
+XKX
+XDP
+DAX
+AXK
+XKQ
+PIX
+IXX
+XXF
+VLX
+XDI
+DIX
+IXL
+XLK
+LKX
+KXV
+XVA
+DNX
+NXD
+ILX
+LXK
+XKV
+VYX
+YXE
+XEI
+RXS
+XSH
+KGX
+XGF
+AVX
+VXY
+XYG
+HVX
+XXI
+XID
+TVX
+XXS
+XSA
+ENX
+NXX
+XMD
+IIX
+XMQ
+AEX
+EXX
+XME
+PGX
+GXP
+XPR
+SKX
+KXF
+XFT
+HRX
+XSW
+PQX
+XGR
+QQX
+VTX
+XRP
+PSX
+SXP
+XPL
+VGX
+GXY
+RSX
+SXS
+XSL
+VSX
+XST
+AXV
+XVL
+AGX
+GXX
+XTK
+KLX
+LXR
+XRV
+AHX
+HXC
+XCS
+LVX
+VXN
+XNR
+NGX
+GXL
+TSX
+SXQ
+XQN
+KXL
+XLL
+VIX
+IXG
+XGA
+GFX
+FXG
+XGL
+PTX
+TXT
+XTS
+EMX
+MXQ
+SXY
+XYA
+IQX
+QXY
+XYR
+TXK
+IGX
+XPS
+PXT
+XTG
+NXQ
+VKX
+KXS
+XSN
+GVX
+VXE
+GRX
+XRE
+YKX
+KXE
+XEE
+EEX
+EXT
+XTI
+EHX
+HXN
+XNL
+NDX
+DXD
+IAX
+KSX
+SXL
+RRX
+XRK
+DDX
+DXE
+RXG
+VXL
+XLS
+DTX
+TXG
+VXF
+XFA
+XIG
+VXT
+XTA
+ISX
+SXR
+XRY
+VQX
+QXP
+XPC
+LGX
+GXS
+HGX
+XGH
+XXD
+XDD
+KKX
+XXV
+PKX
+XLT
+XSP
+XLD
+RAX
+AXS
+XSI
+IYX
+YXX
+XXP
+XPI
+MSX
+SXT
+GEX
+XHP
+LFX
+FXX
+VXI
+XIW
+QTX
+TXX
+XXQ
+XQA
+FLX
+DXN
+XNC
+MXS
+XSR
+YLX
+EQX
+QXS
+TMX
+MXC
+XCY
+NXA
+XAV
+EXE
+XEQ
+HPX
+PXP
+LMX
+MXX
+KTX
+XKK
+XXH
+XHS
+MKX
+XIH
+WRX
+XKS
+EXY
+XYQ
+QKX

chebai/preprocessing/datasets/base.py

@@ -728,7 +728,7 @@ def prepare_data(self, *args: Any, **kwargs: Any) -> None:
 
         processed_name = self.processed_main_file_names_dict["data"]
         if not os.path.isfile(os.path.join(self.processed_dir_main, processed_name)):
-            print("Missing processed data file (`data.pkl` file)")
+            print(f"Missing processed data file (`{processed_name}` file)")
             os.makedirs(self.processed_dir_main, exist_ok=True)
             data_path = self._download_required_data()
             g = self._extract_class_hierarchy(data_path)
@@ -812,12 +812,15 @@ def setup_processed(self) -> None:
             None
         """
         os.makedirs(self.processed_dir, exist_ok=True)
-        print("Missing transformed data (`data.pt` file). Transforming data.... ")
+        processed_main_file_name = self.processed_main_file_names_dict["data"]
+        print(
+            f"Missing transformed data (`{processed_main_file_name}` file). Transforming data.... "
+        )
         torch.save(
             self._load_data_from_file(
                 os.path.join(
                     self.processed_dir_main,
-                    self.processed_main_file_names_dict["data"],
+                    processed_main_file_name,
                 )
             ),
             os.path.join(self.processed_dir, self.processed_file_names_dict["data"]),