modify data process

woreom · Dec 14, 2020 · c9b6ccb · c9b6ccb
1 parent 3d3ada1
commit c9b6ccb
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Showing 240 changed files with 51 additions and 10 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,8 +1,10 @@
 examples/runs
 examples/ft
 examples/results
+examples/data_old
 examples/data
 examples/result
+examples/models
 src/transformers/data/__pycache__
 src/transformers/data/metrics/__pycache__
 src/transformers/data/processors/__pycache__

diff --git a/README.md b/README.md
diff --git a/SNP/SNP.py b/SNP/SNP.py
diff --git a/SNP/example_mut_file.txt b/SNP/example_mut_file.txt
diff --git a/SNP/examples/dev.tsv b/SNP/examples/dev.tsv
diff --git a/SNP/mutate_seqs.py b/SNP/mutate_seqs.py
diff --git a/examples/.Rhistory b/examples/.Rhistory
diff --git a/examples/compute_result.py b/examples/compute_result.py
diff --git a/examples/data_process_template/__pycache__/process_pretrain_data.cpython-36.pyc b/examples/data_process_template/__pycache__/process_pretrain_data.cpython-36.pyc
diff --git a/examples/data_process_template/__pycache__/process_pretrain_data.cpython-38.pyc b/examples/data_process_template/__pycache__/process_pretrain_data.cpython-38.pyc
diff --git a/examples/data_process_template/process_690.py b/examples/data_process_template/process_690.py
diff --git a/examples/data_process_template/process_csv.py b/examples/data_process_template/process_csv.py
@@ -126,8 +126,8 @@ def write_file(lines, writer, seq_index=2, label_index=3):
                 max_length = len(sentence.split())
             writer.writerow([sentence, str(line[label_index])])
 
-    write_file(train_lines, train_w)
-    write_file(test_lines, test_w)
+    write_file(train_lines, train_w, args.seq_index, args.label_index)
+    write_file(test_lines, test_w, args.seq_index, args.label_index)
 
     if args.dev:
         write_file(dev_lines, dev_w)
@@ -170,6 +170,18 @@ def main():
         action="store_true",
         help="Use this flag to split data as (8:1:1), else (9:1)",
     )
+    parser.add_argument(
+        "--seq_index",
+        default=2,
+        type=int,
+        help="index of seq in the original csv file",
+    )
+    parser.add_argument(
+        "--label_index",
+        default=3,
+        type=int,
+        help="index of label in the original csv file",
+    )
     args = parser.parse_args()
 
     if args.pair:
@@ -179,4 +191,4 @@ def main():
 
 
 if __name__ == "__main__":
-    main()
+    main()
diff --git a/examples/data_process_template/process_finetune_data.py b/examples/data_process_template/process_finetune_data.py
@@ -607,9 +607,9 @@ def Process(args):
             os.makedirs(root_path)
 
     old_file =  open(args.file_path, "r", encoding="utf-8-sig")
-    lines = list(csv.reader(old_file, delimiter="\t", quotechar=None))
+    lines = list(csv.reader(old_file, delimiter=args.delimiter, quotechar=None))
 
-    write_file(lines, output_path, args.kmer)
+    write_file(lines, output_path, args.kmer, head=args.head, seq_index=args.seq_index, label_index=args.label_index)
 
 
 def main():
@@ -628,7 +628,7 @@ def main():
     )
     parser.add_argument(
         "--task",
-        default="generate_prom",
+        default="",
         type=str,
         help="which task to do",
     )
@@ -644,11 +644,34 @@ def main():
         type=str,
         help="The path of the processed data",
     )
+    parser.add_argument(
+        "--delimiter",
+        default=',',
+        type=str,
+        help="The path of the processed data",
+    )
+    parser.add_argument(
+        "--head",
+        action="store_true",
+        help="The path of the processed data",
+    )
     parser.add_argument(
         "--dev",
         action="store_true",
         help="Use this flag to split data as (8:1:1), else (9:1)",
     )
+    parser.add_argument(
+        "--seq_index",
+        default=2,
+        type=int,
+        help="index of seq in the original csv file",
+    )
+    parser.add_argument(
+        "--label_index",
+        default=3,
+        type=int,
+        help="index of label in the original csv file",
+    )
     args = parser.parse_args()
 
     if args.task == "generate_prom":

diff --git a/examples/data_process_template/process_ner.py b/examples/data_process_template/process_ner.py
diff --git a/examples/data_process_template/process_pretrain_data.py b/examples/data_process_template/process_pretrain_data.py
diff --git a/examples/data_process_template/process_pretrain_data_multi.py b/examples/data_process_template/process_pretrain_data_multi.py
diff --git a/examples/data_process_template/process_scan_prom_data.py b/examples/data_process_template/process_scan_prom_data.py
diff --git a/examples/requirements.txt b/examples/requirements.txt
@@ -8,3 +8,4 @@ statsmodels
 biopython
 pandas
 pybedtools
+sentencepiece==0.1.91
diff --git a/examples/run_finetune.py b/examples/run_finetune.py
@@ -1081,6 +1081,7 @@ def main():
             config=config,
             cache_dir=args.cache_dir if args.cache_dir else None,
         )
+        logger.info('finish loading model')
 
         if args.local_rank == 0:
             torch.distributed.barrier()  # Make sure only the first process in distributed training will download model & vocab

diff --git a/examples/run_pretrain.py b/examples/run_pretrain.py
diff --git a/examples/sample_data/ft/prom-core/6/dev.tsv b/examples/sample_data/ft/prom-core/6/dev.tsv
diff --git a/examples/sample_data/ft/prom-core/6/train.tsv b/examples/sample_data/ft/prom-core/6/train.tsv
diff --git a/examples/sample_data/pre/6_3k.txt b/examples/sample_data/pre/6_3k.txt
diff --git a/examples/scripts/run_mut.sh b/examples/scripts/run_mut.sh
diff --git a/examples/visualize.py b/examples/visualize.py
diff --git a/motif/find_motifs.py b/motif/find_motifs.py
diff --git a/motif/motif_utils.py b/motif/motif_utils.py
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
diff --git a/src/transformers.egg-info/PKG-INFO b/src/transformers.egg-info/PKG-INFO
@@ -7,7 +7,7 @@ Author: Thomas Wolf, Lysandre Debut, Victor Sanh, Julien Chaumond, Sam Shleifer,
 Author-email: [email protected]
 License: Apache
 Description: # DNABERT
-        This repository includes the implementation of 'DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome'. Please cite our paper if you use the models or codes. The repo is still under developing, so please kindly let us know if there is any issue.
+        This repository includes the implementation of 'DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome'. Please cite our paper if you use the models or codes. The repo is still actively under development, so please kindly report if there is any issue encountered.
 
          In this package, we provides resources including: source codes of the DNABERT model, usage examples, pre-trained models, fine-tuned models and visulization tool. This package is still under development, as more features will be included gradually. Training of DNABERT consists of general-purposed pre-training and task-specific fine-tuning. As a contribution of our project, we released the pre-trained models in this repository. We extended codes from [huggingface](https://github.com/huggingface/transformers) and adapted them to the DNA scenario.
 
@@ -79,7 +79,7 @@ Description: # DNABERT
         export SOURCE=PATH_TO_DNABERT_REPO
         export OUTPUT_PATH=output$KMER
 
-        python run_pretraining.py \
+        python run_pretrain.py \
             --output_dir $OUTPUT_PATH \
             --model_type=dna \
             --tokenizer_name=dna$KMER \
@@ -268,7 +268,7 @@ Description: # DNABERT
             --min_n_motif 3 \
             --align_all_ties \
             --save_file_dir $MOTIF_PATH \
-            --verbose \
+            --verbose
         ```
 
         The script will generate a .txt file and a weblogo .png file for each motif under `MOTIF_PATH`.

diff --git a/src/transformers.egg-info/SOURCES.txt b/src/transformers.egg-info/SOURCES.txt
diff --git a/src/transformers.egg-info/dependency_links.txt b/src/transformers.egg-info/dependency_links.txt
diff --git a/src/transformers.egg-info/requires.txt b/src/transformers.egg-info/requires.txt
diff --git a/src/transformers.egg-info/top_level.txt b/src/transformers.egg-info/top_level.txt
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diff --git a/src/transformers/__pycache__/configuration_albert.cpython-37.pyc b/src/transformers/__pycache__/configuration_albert.cpython-37.pyc
diff --git a/src/transformers/__pycache__/configuration_auto.cpython-37.pyc b/src/transformers/__pycache__/configuration_auto.cpython-37.pyc
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diff --git a/src/transformers/commands/download.py b/src/transformers/commands/download.py
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diff --git a/src/transformers/configuration_transfo_xl.py b/src/transformers/configuration_transfo_xl.py
diff --git a/src/transformers/configuration_utils.py b/src/transformers/configuration_utils.py
diff --git a/src/transformers/configuration_xlm.py b/src/transformers/configuration_xlm.py
diff --git a/src/transformers/configuration_xlm_roberta.py b/src/transformers/configuration_xlm_roberta.py
diff --git a/src/transformers/configuration_xlnet.py b/src/transformers/configuration_xlnet.py
diff --git a/src/transformers/convert_albert_original_tf_checkpoint_to_pytorch.py b/src/transformers/convert_albert_original_tf_checkpoint_to_pytorch.py
diff --git a/src/transformers/convert_bart_original_pytorch_checkpoint_to_pytorch.py b/src/transformers/convert_bart_original_pytorch_checkpoint_to_pytorch.py
diff --git a/src/transformers/convert_bert_pytorch_checkpoint_to_original_tf.py b/src/transformers/convert_bert_pytorch_checkpoint_to_original_tf.py
diff --git a/src/transformers/convert_pytorch_checkpoint_to_tf2.py b/src/transformers/convert_pytorch_checkpoint_to_tf2.py
diff --git a/src/transformers/convert_roberta_original_pytorch_checkpoint_to_pytorch.py b/src/transformers/convert_roberta_original_pytorch_checkpoint_to_pytorch.py
diff --git a/src/transformers/data/__init__.py b/src/transformers/data/__init__.py
diff --git a/src/transformers/data/__pycache__/__init__.cpython-37.pyc b/src/transformers/data/__pycache__/__init__.cpython-37.pyc
diff --git a/src/transformers/data/metrics/__init__.py b/src/transformers/data/metrics/__init__.py
@@ -101,8 +101,10 @@ def glue_compute_metrics(task_name, preds, labels, probs=None):
             return {"mcc": matthews_corrcoef(labels, preds)}
         elif task_name == "sst-2":
             return {"acc": simple_accuracy(preds, labels)}
-        elif task_name in ["dnaprom", "dna690", "dnapair"]:
+        elif task_name in ["dna690", "dnapair"]:
             return acc_f1_mcc_auc_aupr_pre_rec(preds, labels, probs)
+        elif task_name == "dnaprom":
+            return {"acc": simple_accuracy(preds, labels)}
         elif task_name == "dnasplice":
             return acc_f1_mcc_auc_pre_rec(preds, labels, probs)
         elif task_name == "mrpc":

diff --git a/src/transformers/data/metrics/__pycache__/__init__.cpython-37.pyc b/src/transformers/data/metrics/__pycache__/__init__.cpython-37.pyc
diff --git a/src/transformers/data/metrics/squad_metrics.py b/src/transformers/data/metrics/squad_metrics.py
diff --git a/src/transformers/data/processors/__init__.py b/src/transformers/data/processors/__init__.py
diff --git a/src/transformers/data/processors/__pycache__/__init__.cpython-37.pyc b/src/transformers/data/processors/__pycache__/__init__.cpython-37.pyc
diff --git a/src/transformers/data/processors/__pycache__/glue.cpython-37.pyc b/src/transformers/data/processors/__pycache__/glue.cpython-37.pyc
diff --git a/src/transformers/data/processors/__pycache__/squad.cpython-37.pyc b/src/transformers/data/processors/__pycache__/squad.cpython-37.pyc
diff --git a/src/transformers/data/processors/__pycache__/utils.cpython-37.pyc b/src/transformers/data/processors/__pycache__/utils.cpython-37.pyc
diff --git a/src/transformers/data/processors/__pycache__/xnli.cpython-37.pyc b/src/transformers/data/processors/__pycache__/xnli.cpython-37.pyc
diff --git a/src/transformers/data/processors/glue.py b/src/transformers/data/processors/glue.py
diff --git a/src/transformers/data/processors/squad.py b/src/transformers/data/processors/squad.py
diff --git a/src/transformers/data/processors/utils.py b/src/transformers/data/processors/utils.py
diff --git a/src/transformers/data/processors/xnli.py b/src/transformers/data/processors/xnli.py
diff --git a/src/transformers/dnabert-config/bert-config-3/config.json b/src/transformers/dnabert-config/bert-config-3/config.json
diff --git a/src/transformers/dnabert-config/bert-config-3/special_tokens_map.json b/src/transformers/dnabert-config/bert-config-3/special_tokens_map.json
diff --git a/src/transformers/dnabert-config/bert-config-3/tokenizer_config.json b/src/transformers/dnabert-config/bert-config-3/tokenizer_config.json
diff --git a/src/transformers/dnabert-config/bert-config-3/vocab.txt b/src/transformers/dnabert-config/bert-config-3/vocab.txt
diff --git a/src/transformers/dnabert-config/bert-config-4/config.json b/src/transformers/dnabert-config/bert-config-4/config.json
diff --git a/src/transformers/dnabert-config/bert-config-4/special_tokens_map.json b/src/transformers/dnabert-config/bert-config-4/special_tokens_map.json
diff --git a/src/transformers/dnabert-config/bert-config-4/tokenizer_config.json b/src/transformers/dnabert-config/bert-config-4/tokenizer_config.json
diff --git a/src/transformers/dnabert-config/bert-config-4/vocab.txt b/src/transformers/dnabert-config/bert-config-4/vocab.txt
diff --git a/src/transformers/dnabert-config/bert-config-5/config.json b/src/transformers/dnabert-config/bert-config-5/config.json
diff --git a/src/transformers/dnabert-config/bert-config-5/special_tokens_map.json b/src/transformers/dnabert-config/bert-config-5/special_tokens_map.json
diff --git a/src/transformers/dnabert-config/bert-config-5/tokenizer_config.json b/src/transformers/dnabert-config/bert-config-5/tokenizer_config.json
diff --git a/src/transformers/dnabert-config/bert-config-5/vocab.txt b/src/transformers/dnabert-config/bert-config-5/vocab.txt
diff --git a/src/transformers/dnabert-config/bert-config-6/config.json b/src/transformers/dnabert-config/bert-config-6/config.json
diff --git a/src/transformers/dnabert-config/bert-config-6/special_tokens_map.json b/src/transformers/dnabert-config/bert-config-6/special_tokens_map.json
diff --git a/src/transformers/dnabert-config/bert-config-6/tokenizer_config.json b/src/transformers/dnabert-config/bert-config-6/tokenizer_config.json
diff --git a/src/transformers/dnabert-config/bert-config-6/vocab.txt b/src/transformers/dnabert-config/bert-config-6/vocab.txt
diff --git a/src/transformers/file_utils.py b/src/transformers/file_utils.py
diff --git a/src/transformers/hf_api.py b/src/transformers/hf_api.py
diff --git a/src/transformers/modelcard.py b/src/transformers/modelcard.py
diff --git a/src/transformers/modeling_albert.py b/src/transformers/modeling_albert.py
diff --git a/src/transformers/modeling_auto.py b/src/transformers/modeling_auto.py
diff --git a/src/transformers/modeling_bart.py b/src/transformers/modeling_bart.py
diff --git a/src/transformers/modeling_bert.py b/src/transformers/modeling_bert.py
diff --git a/src/transformers/modeling_camembert.py b/src/transformers/modeling_camembert.py
diff --git a/src/transformers/modeling_ctrl.py b/src/transformers/modeling_ctrl.py
diff --git a/src/transformers/modeling_distilbert.py b/src/transformers/modeling_distilbert.py
diff --git a/src/transformers/modeling_encoder_decoder.py b/src/transformers/modeling_encoder_decoder.py
diff --git a/src/transformers/modeling_flaubert.py b/src/transformers/modeling_flaubert.py
diff --git a/src/transformers/modeling_gpt2.py b/src/transformers/modeling_gpt2.py
diff --git a/src/transformers/modeling_mmbt.py b/src/transformers/modeling_mmbt.py
diff --git a/src/transformers/modeling_openai.py b/src/transformers/modeling_openai.py
diff --git a/src/transformers/modeling_roberta.py b/src/transformers/modeling_roberta.py
diff --git a/src/transformers/modeling_t5.py b/src/transformers/modeling_t5.py
diff --git a/src/transformers/modeling_tf_albert.py b/src/transformers/modeling_tf_albert.py
diff --git a/src/transformers/modeling_tf_auto.py b/src/transformers/modeling_tf_auto.py
diff --git a/src/transformers/modeling_tf_bert.py b/src/transformers/modeling_tf_bert.py
diff --git a/src/transformers/modeling_tf_camembert.py b/src/transformers/modeling_tf_camembert.py
diff --git a/src/transformers/modeling_tf_ctrl.py b/src/transformers/modeling_tf_ctrl.py
diff --git a/src/transformers/modeling_tf_distilbert.py b/src/transformers/modeling_tf_distilbert.py
diff --git a/src/transformers/modeling_tf_gpt2.py b/src/transformers/modeling_tf_gpt2.py
diff --git a/src/transformers/modeling_tf_openai.py b/src/transformers/modeling_tf_openai.py
diff --git a/src/transformers/modeling_tf_pytorch_utils.py b/src/transformers/modeling_tf_pytorch_utils.py
diff --git a/src/transformers/modeling_tf_roberta.py b/src/transformers/modeling_tf_roberta.py
diff --git a/src/transformers/modeling_tf_t5.py b/src/transformers/modeling_tf_t5.py
diff --git a/src/transformers/modeling_tf_transfo_xl.py b/src/transformers/modeling_tf_transfo_xl.py
diff --git a/src/transformers/modeling_tf_transfo_xl_utilities.py b/src/transformers/modeling_tf_transfo_xl_utilities.py
diff --git a/src/transformers/modeling_tf_utils.py b/src/transformers/modeling_tf_utils.py
diff --git a/src/transformers/modeling_tf_xlm.py b/src/transformers/modeling_tf_xlm.py
diff --git a/src/transformers/modeling_tf_xlm_roberta.py b/src/transformers/modeling_tf_xlm_roberta.py
diff --git a/src/transformers/modeling_tf_xlnet.py b/src/transformers/modeling_tf_xlnet.py
diff --git a/src/transformers/modeling_transfo_xl.py b/src/transformers/modeling_transfo_xl.py
diff --git a/src/transformers/modeling_transfo_xl_utilities.py b/src/transformers/modeling_transfo_xl_utilities.py
diff --git a/src/transformers/modeling_utils.py b/src/transformers/modeling_utils.py
diff --git a/src/transformers/modeling_xlm.py b/src/transformers/modeling_xlm.py
diff --git a/src/transformers/modeling_xlm_roberta.py b/src/transformers/modeling_xlm_roberta.py
diff --git a/src/transformers/modeling_xlnet.py b/src/transformers/modeling_xlnet.py
diff --git a/src/transformers/optimization.py b/src/transformers/optimization.py
diff --git a/src/transformers/optimization_tf.py b/src/transformers/optimization_tf.py
diff --git a/src/transformers/tokenization_albert.py b/src/transformers/tokenization_albert.py
diff --git a/src/transformers/tokenization_auto.py b/src/transformers/tokenization_auto.py
diff --git a/src/transformers/tokenization_bart.py b/src/transformers/tokenization_bart.py
diff --git a/src/transformers/tokenization_bert.py b/src/transformers/tokenization_bert.py
diff --git a/src/transformers/tokenization_bert_japanese.py b/src/transformers/tokenization_bert_japanese.py
diff --git a/src/transformers/tokenization_camembert.py b/src/transformers/tokenization_camembert.py
diff --git a/src/transformers/tokenization_ctrl.py b/src/transformers/tokenization_ctrl.py
diff --git a/src/transformers/tokenization_distilbert.py b/src/transformers/tokenization_distilbert.py
diff --git a/src/transformers/tokenization_dna.py b/src/transformers/tokenization_dna.py
diff --git a/src/transformers/tokenization_flaubert.py b/src/transformers/tokenization_flaubert.py
diff --git a/src/transformers/tokenization_gpt2.py b/src/transformers/tokenization_gpt2.py
diff --git a/src/transformers/tokenization_openai.py b/src/transformers/tokenization_openai.py
diff --git a/src/transformers/tokenization_roberta.py b/src/transformers/tokenization_roberta.py
diff --git a/src/transformers/tokenization_t5.py b/src/transformers/tokenization_t5.py
diff --git a/src/transformers/tokenization_transfo_xl.py b/src/transformers/tokenization_transfo_xl.py
diff --git a/src/transformers/tokenization_utils.py b/src/transformers/tokenization_utils.py
diff --git a/src/transformers/tokenization_xlm.py b/src/transformers/tokenization_xlm.py
diff --git a/src/transformers/tokenization_xlm_roberta.py b/src/transformers/tokenization_xlm_roberta.py
diff --git a/src/transformers/tokenization_xlnet.py b/src/transformers/tokenization_xlnet.py
diff --git a/src/transformers/utils_encoder_decoder.py b/src/transformers/utils_encoder_decoder.py