ruff format

dscript/commands/embed.py

@@ -29,8 +29,11 @@ def add_args(parser):
     parser.add_argument("--seqs", help="Sequences to be embedded", required=True)
     parser.add_argument("-o", "--outfile", help="h5 file to write results", required=True)
     parser.add_argument(
-        "-d", "--device", type=str, default="cpu", 
-        help="Compute device to use. Options: 'cpu' or GPU index (0, 1, 2, etc.)."
+        "-d",
+        "--device",
+        type=str,
+        default="cpu",
+        help="Compute device to use. Options: 'cpu' or GPU index (0, 1, 2, etc.).",
     )
     return parser
 
@@ -45,11 +48,13 @@ def main(args):
     outPath = args.outfile
     device_arg = args.device
     if device_arg.lower() == "cpu":
-        device = -1 #Refers to CPU in embed_from_fasta
+        device = -1  # Refers to CPU in embed_from_fasta
     elif device_arg.isdigit():  # Allow only nonnegative integers
         device = int(device_arg)
     else:
-        log(f"Invalid device argument: {device_arg}. Use 'cpu' or a GPU index. Using CPU.")
+        log(
+            f"Invalid device argument: {device_arg}. Use 'cpu' or a GPU index. Using CPU."
+        )
         device = -1
     embed_from_fasta(inPath, outPath, device, verbose=True)
 

dscript/commands/predict_serial.py

@@ -62,8 +62,11 @@ def add_args(parser):
     )
     parser.add_argument("-o", "--outfile", help="File for predictions")
     parser.add_argument(
-        "-d", "--device", type=str, default="cpu", 
-        help="Compute device to use. Options: 'cpu' or GPU index (0, 1, 2, etc.)."
+        "-d",
+        "--device",
+        type=str,
+        default="cpu",
+        help="Compute device to use. Options: 'cpu' or GPU index (0, 1, 2, etc.).",
     )
     parser.add_argument(
         "--store_cmaps",
@@ -102,11 +105,13 @@ def main(args):
     embPath = args.embeddings
     device_arg = args.device
     if device_arg.lower() == "cpu":
-        device = -1 #Refers to CPU in embed_from_fasta
+        device = -1  # Refers to CPU in embed_from_fasta
     elif device_arg.isdigit():  # Allow only nonnegative integers
         device = int(device_arg)
     else:
-        log(f"Invalid device argument: {device_arg}. Use 'cpu' or a GPU index. Using CPU.")
+        log(
+            f"Invalid device argument: {device_arg}. Use 'cpu' or a GPU index. Using CPU."
+        )
         device = -1
     threshold = args.thresh
 
@@ -120,7 +125,9 @@ def main(args):
     logFile = open(logFilePath, "w+")
 
     # Set Device
-    use_cuda = (device >= 0) and torch.cuda.is_available() and device < torch.cuda.device_count()
+    use_cuda = (
+        (device >= 0) and torch.cuda.is_available() and device < torch.cuda.device_count()
+    )
     if use_cuda:
         torch.cuda.set_device(device)
         log(

dscript/language_model.py

@@ -54,7 +54,9 @@ def embed_from_fasta(fastaPath, outputPath, device=0, verbose=False):
     :param verbose: Print embedding progress
     :type verbose: bool
     """
-    use_cuda = (device >= 0) and torch.cuda.is_available() and device < torch.cuda.device_count()
+    use_cuda = (
+        (device >= 0) and torch.cuda.is_available() and device < torch.cuda.device_count()
+    )
     if use_cuda:
         torch.cuda.set_device(device)
         if verbose:

scripts/bmpi_bench/sample_pairs.py

@@ -1,14 +1,13 @@
 import random
-import sys 
+import sys
 
 f = open(sys.argv[1])
 prots = [x.strip() for x in f.readlines()]
-pairs = [(p, q) for i, p in enumerate(prots) for q in prots[i+1:]]
+pairs = [(p, q) for i, p in enumerate(prots) for q in prots[i + 1 :]]
 np = len(pairs)
-target = int(float(sys.argv[2])*np)
+target = int(float(sys.argv[2]) * np)
 print(f"Choosing {target} pairs from {np}", file=sys.stderr)
 random.seed(0)
 sel = random.sample(range(np), k=target)
 for i in sel:
     print(*pairs[i], sep="\t")
-

scripts/bmpi_bench/select_dmel_seqs.py

@@ -1,12 +1,12 @@
 import sys
-#args: isoform table, fasta, output table, output fasta, max length, output filtered fasta
+# args: isoform table, fasta, output table, output fasta, max length, output filtered fasta
 
 prots = set()
 genes = set()
 
 with open(sys.argv[1]) as isoforms:
     for line in isoforms:
-        if line.isspace() or line[0] == "#" or not(line): 
+        if line.isspace() or line[0] == "#" or not (line):
             continue
         tokens = line.strip().split()
         gene = tokens[0]
@@ -29,16 +29,16 @@ else:
 
 with open(sys.argv[2]) as fasta:
     for line in fasta:
-        if line.isspace() or line[0] == "#" or not(line):
+        if line.isspace() or line[0] == "#" or not (line):
             continue
         if line[0] == ">":
             if collect:
                 collect = False
                 l = len(seqbuffer)
                 print(id, name, l, sep="\t", file=outTable)
-                print(">"+id, seqbuffer, sep="\n", file=outFasta)
+                print(">" + id, seqbuffer, sep="\n", file=outFasta)
                 if filter and l <= thresh:
-                    print(">"+id, seqbuffer, sep="\n", file=outFilter)
+                    print(">" + id, seqbuffer, sep="\n", file=outFilter)
                 seqbuffer = ""
                 id = ""
                 name = ""
@@ -57,15 +57,9 @@ with open(sys.argv[2]) as fasta:
 if collect:
     l = len(seqbuffer)
     print(id, name, l, sep="\t", file=outTable)
-    print(">"+id, seqbuffer, sep="\n", file=outFasta)
+    print(">" + id, seqbuffer, sep="\n", file=outFasta)
     if filter and l <= thresh:
-        print(">"+id, seqbuffer, sep="\n", file=outFilter)
+        print(">" + id, seqbuffer, sep="\n", file=outFilter)
 outTable.close()
 outFasta.close()
 outFilter.close()
-
-
-
-
-        
-

scripts/bmpi_bench/select_endo_seqs.py

@@ -1,5 +1,5 @@
 import sys
-#args: fasta, min length, max length, output table,  output filtered fasta
+# args: fasta, min length, max length, output table,  output filtered fasta
 
 
 collect = False
@@ -11,7 +11,7 @@ thresh = int(sys.argv[3])
 floor = int(sys.argv[2])
 with open(sys.argv[1]) as fasta:
     for line in fasta:
-        if line.isspace() or line[0] == "#" or not(line):
+        if line.isspace() or line[0] == "#" or not (line):
             continue
         if line[0] == ">":
             if collect:
@@ -19,7 +19,7 @@ with open(sys.argv[1]) as fasta:
                 l = len(seqbuffer)
                 print(name, l, sep="\t", file=outTable)
                 if l >= floor and l <= thresh:
-                    print(">"+name, seqbuffer, sep="\n", file=outFilter)
+                    print(">" + name, seqbuffer, sep="\n", file=outFilter)
                 seqbuffer = ""
                 name = ""
             name = line.split()[0][1:]
@@ -30,12 +30,6 @@ if collect:
     l = len(seqbuffer)
     print(name, l, sep="\t", file=outTable)
     if l >= floor and l <= thresh:
-        print(">"+name, seqbuffer, sep="\n", file=outFilter)
+        print(">" + name, seqbuffer, sep="\n", file=outFilter)
 outTable.close()
 outFilter.close()
-
-
-
-
-        
-