Merge pull request #16 from jamaliki/main-pr

Fix hmmsearch

install_script.sh

@@ -42,7 +42,7 @@ then
   exit 1;
 fi
 
-conda install -y pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch
+conda install -y pytorch torchvision torchaudio cudatoolkit=11.7 -c pytorch
 
 if [ "${torch_home_path}" ]
 then

model_angelo/apps/hmm_search.py

@@ -143,11 +143,9 @@ def main(parsed_args):
     os.makedirs(parsed_args.output_dir, exist_ok=True)
 
     pruned_hmms = [k for k in hmms if k[1].alphabet == alphabet]
-    with pyhmmer.easel.SequenceFile(
-        parsed_args.fasta_path, alphabet=alphabet, digital=True
-    ) as sf:
-        digital_sequences = list(sf)
-    print(digital_sequences[0])
+
+    with pyhmmer.easel.SequenceFile(parsed_args.fasta_path, alphabet=alphabet, digital=True) as sf:
+        digital_sequences = sf.read_block()
 
     pipeline = pyhmmer.plan7.Pipeline(
         alphabet,
@@ -158,14 +156,15 @@ def main(parsed_args):
         T=parsed_args.T,
     )
     for (name, hmm) in tqdm.tqdm(pruned_hmms):
-        hits = pipeline.search_hmm(hmm, digital_sequences)
-
+        try:
+            hits = pipeline.search_hmm(hmm, digital_sequences)
+        except Exception as e:
+            print(f"Chain {name} failed")
+            continue
         if parsed_args.pipeline_control:
             abort_if_relion_abort(parsed_args.output_dir)
-
         with open(os.path.join(parsed_args.output_dir, f"{name}.hhr"), "wb") as f:
             hits.write(f)
-
         try:
             msa = hits.to_msa(alphabet)
             with open(os.path.join(parsed_args.output_dir, f"{name}.a2m"), "wb") as f:

requirements.txt

@@ -6,5 +6,5 @@ matplotlib
 mrcfile
 pandas
 fair-esm
-pyhmmer
-loguru
+pyhmmer >= 0.7.1
+loguru

todos.md

@@ -0,0 +1,7 @@
+# Todo's
+
+- [ ] Proper error catching for shape errors, issues with FASTA files, etc
+- [ ] Test fully if the poly-A works. Extend to proteins perhaps?
+- [ ] Refinement program
+- [ ] Do not run segmentation on masked out areas
+- [ ] Switch poly-A nucleotide to poly-U (or any pyrimidine)