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Adibvafa · Aug 23, 2024 · 6f3a500 · 6f3a500
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Showing 4 changed files with 22 additions and 56 deletions.
diff --git a/CodonTransformer/CodonData.py b/CodonTransformer/CodonData.py
@@ -345,10 +345,12 @@ def get_amino_acid_sequence(
             table=codon_table,  # Codon table to use for translation
         )
     ).strip()
-
-    return protein_seq \
-            if not return_correct_seq \
-            else (protein_seq, is_correct_seq(dna_seq, protein_seq, stop_symbol))
+
+    return (
+        protein_seq
+        if not return_correct_seq
+        else (protein_seq, is_correct_seq(dna_seq, protein_seq, stop_symbol))
+    )
 
 
 def read_fasta_file(
@@ -399,7 +401,10 @@ def read_fasta_file(
 
             # Translate DNA to protein sequence
             protein, correct_seq = get_amino_acid_sequence(
-                dna, stop_symbol=STOP_SYMBOL, codon_table=codon_table, return_correct_seq=True
+                dna,
+                stop_symbol=STOP_SYMBOL,
+                codon_table=codon_table,
+                return_correct_seq=True,
             )
             description = str(record.description[: record.description.find("[")])
             tokenized = get_merged_seq(protein, dna, seperator=STOP_SYMBOL)

diff --git a/CodonTransformer/CodonEvaluation.py b/CodonTransformer/CodonEvaluation.py
@@ -11,8 +11,6 @@
 from typing import List, Dict, Tuple
 from tqdm import tqdm
 
-from CodonTransformer.CodonUtils import AMINO2CODON_TYPE
-from CodonTransformer.CodonData import build_amino2codon_skeleton, get_codon_frequencies
 
 
 def get_CSI_weights(sequences: List[str]) -> Dict[str, float]:

diff --git a/finetune.py b/finetune.py
@@ -187,22 +187,13 @@ def main(args):
         help="Filename for the saved checkpoint",
     )
     parser.add_argument(
-        "--batch_size",
-        type=int,
-        default=6,
-        help="Batch size for training"
+        "--batch_size", type=int, default=6, help="Batch size for training"
     )
     parser.add_argument(
-        "--max_epochs",
-        type=int,
-        default=15,
-        help="Maximum number of epochs to train"
+        "--max_epochs", type=int, default=15, help="Maximum number of epochs to train"
     )
     parser.add_argument(
-        "--num_workers",
-        type=int,
-        default=5,
-        help="Number of workers for data loading"
+        "--num_workers", type=int, default=5, help="Number of workers for data loading"
     )
     parser.add_argument(
         "--accumulate_grad_batches",
@@ -211,10 +202,7 @@ def main(args):
         help="Number of batches to accumulate gradients",
     )
     parser.add_argument(
-        "--num_gpus",
-        type=int,
-        default=4,
-        help="Number of GPUs to use for training"
+        "--num_gpus", type=int, default=4, help="Number of GPUs to use for training"
     )
     parser.add_argument(
         "--learning_rate",
@@ -235,10 +223,7 @@ def main(args):
         help="Save checkpoint every N steps",
     )
     parser.add_argument(
-        "--seed",
-        type=int,
-        default=123,
-        help="Random seed for reproducibility"
+        "--seed", type=int, default=123, help="Random seed for reproducibility"
     )
     parser.add_argument("--debug", action="store_true", help="Enable debug mode")
     args = parser.parse_args()

diff --git a/pretrain.py b/pretrain.py
@@ -199,22 +199,13 @@ def main(args):
         help="Directory where checkpoints will be saved",
     )
     parser.add_argument(
-        "--batch_size",
-        type=int,
-        default=6,
-        help="Batch size for training"
+        "--batch_size", type=int, default=6, help="Batch size for training"
     )
     parser.add_argument(
-        "--max_epochs",
-        type=int,
-        default=5,
-        help="Maximum number of epochs to train"
+        "--max_epochs", type=int, default=5, help="Maximum number of epochs to train"
     )
     parser.add_argument(
-        "--num_workers",
-        type=int,
-        default=5,
-        help="Number of workers for data loading"
+        "--num_workers", type=int, default=5, help="Number of workers for data loading"
     )
     parser.add_argument(
         "--accumulate_grad_batches",
@@ -223,10 +214,7 @@ def main(args):
         help="Number of batches to accumulate gradients",
     )
     parser.add_argument(
-        "--num_gpus",
-        type=int,
-        default=16,
-        help="Number of GPUs to use for training"
+        "--num_gpus", type=int, default=16, help="Number of GPUs to use for training"
     )
     parser.add_argument(
         "--learning_rate",
@@ -241,21 +229,11 @@ def main(args):
         help="Fraction of total steps to use for warmup",
     )
     parser.add_argument(
-        "--save_interval",
-        type=int,
-        default=5,
-        help="Save checkpoint every N epochs"
-    )
-    parser.add_argument(
-        "--seed",
-        type=int,
-        default=123,
-        help="Random seed for reproducibility"
+        "--save_interval", type=int, default=5, help="Save checkpoint every N epochs"
     )
     parser.add_argument(
-        "--debug",
-        action="store_true",
-        help="Enable debug mode"
+        "--seed", type=int, default=123, help="Random seed for reproducibility"
     )
+    parser.add_argument("--debug", action="store_true", help="Enable debug mode")
     args = parser.parse_args()
     main(args)