Merge pull request #182 from ziadbkh/visualisation

 Produce an interactive html report for the predecited strucures

bin/extract_output.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+import pickle
+import os
+import argparse
+
+
+def read_pkl(id, pkl_files):
+    for pkl_file in pkl_files:
+        dict_data = pickle.load(open(pkl_file, "rb"))
+        if pkl_file.endswith("features.pkl"):
+            with open(f"{id}_msa.tsv", "w") as out_f:
+                for val in dict_data["msa"]:
+                    out_f.write("\t".join([str(x) for x in val]) + "\n")
+        else:
+            model_id = (
+                os.path.basename(pkl_file)
+                .replace("result_model_", "")
+                .replace("_pred_0.pkl", "")
+            )
+            with open(f"{id}_lddt_{model_id}.tsv", "w") as out_f:
+                out_f.write("\t".join([str(x) for x in dict_data["plddt"]]) + "\n")
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--pkls", dest="pkls", required=True, nargs="+")
+parser.add_argument("--name", dest="name")
+parser.add_argument("--output_dir", dest="output_dir")
+parser.set_defaults(output_dir="")
+parser.set_defaults(name="")
+args = parser.parse_args()
+
+read_pkl(args.name, args.pkls)