updated git_colab_requirements

MixTCRpred.py

@@ -8,6 +8,7 @@
 import configparser
 import pandas as pd
 
+#path_pretrained_models = './pretrained_models'
 path_pretrained_models = './pretrained_models'
 
 if __name__ == '__main__':
@@ -80,7 +81,7 @@
         sys.exit(0)
 
     if args.download != None:
-        print('Downloading TCrpred model for {0})'.format(args.download))
+        print('Downloading MixTCRpred model for {0})'.format(args.download))
         url = "https://zenodo.org/record/7930623/files/model_"+args.download+".ckpt"
         if os.path.exists( os.path.join(path_pretrained_models, "model_{0}.ckpt".format(args.download))):
             print("{0} MixTCRpred model already downloaded".format(args.download))

README.md

@@ -8,7 +8,7 @@ This branch is specifically for the NY-ESO-1<sub>157-165</sub> epitope. As descr
 
 For this MixTCRpred model:
 
-- **Only TCRs with TRBV6-5, TRBJ2-2, beginning with "CASS" and ending with "GELFF" in the CDR3 beta will be accepted as inputs. All other sequences will be discarded.***
+- **Only TCRs with TRBV6-5, TRBJ2-2, beginning with "CASS" and ending with "GELFF" in the CDR3 beta will be accepted as inputs. All other sequences will be discarded.**
 - The alpha chain sequences are not used for predicting the TCR specificity. TCRs with alpha chain sequences equal to the reference TCR used in the phage display screening (TRAV21 | CAVRPTSGGSYIPTF | TRAJ6) are accepted as inputs, while other alpha chains will be replaced by null values.
 
 

colab_MixTCRpred.ipynb

@@ -13,7 +13,7 @@
     "#clone the repository and the data to run the notebook on Google Colab\n",
     "!git clone https://github.com/GfellerLab/MixTCRpred\n",
     "!pip install wget >> /dev/null \n",
-    "!pip install pytorch_lightning==1.6.0 >> /dev/null \n",
+    "!pip install pytorch_lightning >> /dev/null \n",
     "%cd MixTCRpred"
    ]
   },