0.1.7

GPU running fixed

senseppi/__init__.py

-__version__ = "0.1.6"
+__version__ = "0.1.7"
 __author__ = "Konstantin Volzhenin"
 
 from . import model, commands, esm2_model, dataset, utils, network_utils

senseppi/__main__.py

@@ -42,6 +42,8 @@ def main():
         if params.device == 'gpu':
             torch.set_float32_matmul_precision('high')
 
+        logging.info('Device used: {}'.format(params.device))
+
     params.func(params)
 
 

senseppi/esm2_model.py

@@ -47,7 +47,7 @@ def run(args):
     model, alphabet = pretrained.load_model_and_alphabet(args.model_location_esm)
     model.eval()
 
-    if args.device == 'cuda':
+    if args.device == 'gpu':
         model = model.cuda()
         print("Transferred the ESM2 model to GPU")
     elif args.device == 'mps':
@@ -71,7 +71,7 @@ def run(args):
             print(
                 f"Processing {batch_idx + 1} of {len(batches)} batches ({toks.size(0)} sequences)"
             )
-            if args.device == 'cuda':
+            if args.device == 'gpu':
                 toks = toks.to(device="cuda", non_blocking=True)
             elif args.device == 'mps':
                 toks = toks.to(device="mps", non_blocking=True)

senseppi/network_utils.py

@@ -14,6 +14,7 @@ import shutil
 
 DOWNLOAD_LINK_STRING = "https://stringdb-downloads.org/download/"
 
+
 def generate_pairs_string(fasta_file, output_file, with_self=False, delete_proteins=None):
     ids = []
     for record in SeqIO.parse(fasta_file, "fasta"):
@@ -85,7 +86,8 @@ def get_interactions_from_string(gene_names, species=9606, add_nodes=10, require
     # Download protein sequences for given species if not downloaded yet
     if not os.path.isfile('{}.protein.sequences.v{}.fa'.format(species, version)):
         print('Downloading protein sequences')
-        url = '{0}protein.sequences.v{1}/{2}.protein.sequences.v{1}.fa.gz'.format(DOWNLOAD_LINK_STRING, version, species)
+        url = '{0}protein.sequences.v{1}/{2}.protein.sequences.v{1}.fa.gz'.format(DOWNLOAD_LINK_STRING, version,
+                                                                                  species)
         urllib.request.urlretrieve(url, '{}.protein.sequences.v{}.fa.gz'.format(species, version))
         print('Unzipping protein sequences')
         with gzip.open('{}.protein.sequences.v{}.fa.gz'.format(species, version), 'rb') as f_in:
@@ -145,5 +147,6 @@ def get_interactions_from_string(gene_names, species=9606, add_nodes=10, require
                 SeqIO.write(record, f, "fasta")
     string_interactions.to_csv('string_interactions.tsv', sep='\t', index=False)
 
+
 if __name__ == '__main__':
     get_interactions_from_string('RFC5')