0.6.5 updated names for tmp files for esm2 and fasta utils

senseppi/esm2_model.py

@@ -10,6 +10,7 @@ import logging
 from esm import FastaBatchedDataset, pretrained
 from copy import copy
 from Bio import SeqIO
+from datetime import datetime
 
 
 def add_esm_args(parent_parser):
@@ -119,13 +120,19 @@ def compute_embeddings(params):
                 seq_dict.pop(seq_id)
         if len(seq_dict) > 0:
             params_esm = copy(params)
-            params_esm.fasta_file = Path(str(params.fasta_file).replace('fasta', 'tmp.fasta'))
-            with open(params_esm.fasta_file, 'w') as f:
-                for seq_id in seq_dict.keys():
-                    f.write('>' + seq_id + '\n')
-                    f.write(str(seq_dict[seq_id].seq) + '\n')
-            run(params_esm)
-            os.remove(params_esm.fasta_file)
+            try:
+                current_time = str(datetime.now()).replace(' ', '_')
+                params_esm.fasta_file = Path(current_time + '_' + str(params.fasta_file).replace('fasta', 'tmp.fasta'))
+                with open(params_esm.fasta_file, 'w') as f:
+                    for seq_id in seq_dict.keys():
+                        f.write('>' + seq_id + '\n')
+                        f.write(str(seq_dict[seq_id].seq) + '\n')
+                run(params_esm)
+            except Exception as e:
+                raise e
+            finally:
+                if os.path.exists(params_esm.fasta_file):
+                    os.remove(params_esm.fasta_file)
         else:
             logging.info('All ESM embeddings already computed')
 

senseppi/utils.py

@@ -4,6 +4,7 @@ from senseppi import __version__
 import torch
 import logging
 import argparse
+from datetime import datetime
 
 
 class ArgumentParserWithDefaults(argparse.ArgumentParser):
@@ -68,7 +69,8 @@ def block_mps(params):
 
 
 def process_string_fasta(fasta_file, min_len, max_len):
-    with open('file.tmp', 'w') as f:
+    tmp_name = str(datetime.now()).replace(' ', '_') + '_fasta_processed.tmp'
+    with open(tmp_name, 'w') as f:
         for record in SeqIO.parse(fasta_file, "fasta"):
             if len(record.seq) < min_len or len(record.seq) > max_len:
                 continue
@@ -78,7 +80,7 @@ def process_string_fasta(fasta_file, min_len, max_len):
             SeqIO.write(record, f, "fasta")
     # Rename the temporary file to the original file
     os.remove(fasta_file)
-    os.rename('file.tmp', fasta_file)
+    os.rename(tmp_name, fasta_file)
 
 
 def get_fasta_ids(fasta_file):