support small_bfd with ray (#65)

* support small_bfd with ray

* rm useless log

fastfold/data/feature_pipeline.py

@@ -76,7 +76,6 @@ def np_example_to_features(
     mode: str,
 ):
     np_example = dict(np_example)
-    print("np_example seq_length", np_example["seq_length"])
     if is_multimer:
         num_res = int(np_example["seq_length"][0])
     else:

fastfold/workflow/template/fastfold_data_workflow.py

@@ -123,6 +123,7 @@ class FastFoldDataWorkFlow:
         # generate workflow for STEP3
         jh_node_2 = jh_fac.gen_node(fasta_path, mgnify_out_path)
 
+        if not self.use_small_bfd:
             # Run HHBlits on BFD
             # create HHBlits workflow generator
             hhb_config = {
@@ -138,5 +139,16 @@ class FastFoldDataWorkFlow:
 
             # run workflow
             batch_run(workflow_id=workflow_id, dags=[hhs_node, jh_node_2, hhb_node])
+        else:
+            # Run Jackhmmer on small_bfd
+            # reconfigure jackhmmer factory to use small_bfd DB instead
+            jh_fac.configure('database_path', self.db_map["jackhmmer"]["dbs"][2])
+            # set jackhmmer output path
+            bfd_out_path = os.path.join(alignment_dir, "bfd_uniclust_hits.a3m")
+            # generate workflow for STEP4_2
+            jh_node_3 = jh_fac.gen_node(fasta_path, bfd_out_path)
+
+            # run workflow
+            batch_run(workflow_id=workflow_id, dags=[hhs_node, jh_node_2, jh_node_3]) 
 
         return
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