khanhlee / bert-enhancer

A Transformer Architecture Based on BERT and 2D Convolutional Neural Network to Identify DNA Enhancers from Sequence Information
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How to make code automatic for sequence feature extraction #13

Open tabrejmsc opened 1 year ago

tabrejmsc commented 1 year ago

I run the code for one by one sequence and extract the features for one by one sequence means jsonl file to .excel file But i need some favor from your side how we can pass all sequence file to BERT model because this code have only one file example python ./bert/extract_features.py --input_file=./input.txt --output_file=D:/output.jsonl --vocab_file=./vocabs.txt --bert_config_file=./bert_large_L-24_H-1024_A-16_I-512.json --init_checkpoint=./bert_large_L-24_H-1024_A-16_I-512/model.ckpt-1000000.index --do_lower_case=False --layers=-1,-2,-3,-4 --max_seq_length=512 --batch_size=64 Kindly help me regarding this