scottclowe commited on
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1 Parent(s): 2c0808a

DOC: Blacken example code block

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  1. README.md +7 -5
README.md CHANGED
@@ -16,19 +16,21 @@ To use **BarcodeBERT** as a feature extractor:
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  from transformers import AutoTokenizer, AutoModel
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  # Load the tokenizer
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- tokenizer = AutoTokenizer.from_pretrained("bioscan-ml/BarcodeBERT", trust_remote_code=True)
 
 
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- #Load the model
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  model = AutoModel.from_pretrained("bioscan-ml/BarcodeBERT", trust_remote_code=True)
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  # Sample sequence
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- dna_seq = 'ACGCGCTGACGCATCAGCATACGA'
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  # Tokenize
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- input_seq = tokenizer(dna_seq, return_tensors = 'pt')['input_ids']
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  # Pass through the model
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- output = model(input_seq.unsqueeze(0))['hidden_states'][-1]
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  # Compute Global Average Pooling
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  features = output.mean(1)
 
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  from transformers import AutoTokenizer, AutoModel
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  # Load the tokenizer
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+ tokenizer = AutoTokenizer.from_pretrained(
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+ "bioscan-ml/BarcodeBERT", trust_remote_code=True
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+ )
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+ # Load the model
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  model = AutoModel.from_pretrained("bioscan-ml/BarcodeBERT", trust_remote_code=True)
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  # Sample sequence
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+ dna_seq = "ACGCGCTGACGCATCAGCATACGA"
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  # Tokenize
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+ input_seq = tokenizer(dna_seq, return_tensors="pt")["input_ids"]
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  # Pass through the model
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+ output = model(input_seq.unsqueeze(0))["hidden_states"][-1]
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  # Compute Global Average Pooling
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  features = output.mean(1)