tetss2 0.1.0__tar.gz

tetss2-0.1.0/MANIFEST.in

@@ -0,0 +1,2 @@
+recursive-include src/tetss2/assets *.pth
+include README.md

tetss2-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: tetss2
+Version: 0.1.0
+Summary: TETSS2.0: a PyTorch model for predicting TE-TSS activity from DNA sequences.
+Author-email: Moriyaa Cui <2311459@tongji.edu.cn>
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.21
+Requires-Dist: pandas>=1.3
+Requires-Dist: torch>=1.10
+
+# TETSS2.0
+
+**TETSS2.0** is a deep learning model for predicting TE-derived transcription start site (TE-TSS) activity from DNA sequences.
+
+The Python package name and command-line tool name are **`tetss2`**. The model name shown in documents, figures, and the website is **TETSS2.0**.
+
+---
+
+## Overview
+
+TETSS2.0 is a PyTorch-based convolutional neural network classifier designed to predict whether an input DNA sequence is associated with TE-TSS activity.
+
+The model takes a DNA sequence as input and returns:
+
+* a prediction probability
+* a binary prediction label
+* the classification threshold used for prediction
+
+By default, TETSS2.0 uses a threshold of `0.5`.
+
+---
+
+## Input requirement
+
+TETSS2.0 expects DNA sequences of exactly **201 bp**.
+
+Allowed bases:
+
+```text
+A, C, G, T, N
+```
+
+Notes:
+
+* Input sequences are automatically converted to uppercase.
+* `N` is allowed but is encoded as an all-zero position in the one-hot representation.
+* Sequences shorter or longer than 201 bp are rejected by default.
+* The option `--no-length-check` is available only for debugging and is not recommended for normal prediction.
+
+---
+
+## Output
+
+For each input sequence, TETSS2.0 outputs:
+
+| Column                   | Description                              |
+| ------------------------ | ---------------------------------------- |
+| `tetss2_sequence_length` | Length of the input sequence             |
+| `tetss2_probability`     | Predicted probability score              |
+| `tetss2_prediction`      | Binary prediction result, `0` or `1`     |
+| `tetss2_threshold`       | Threshold used for binary classification |
+
+---
+
+## Installation
+
+### Option 1: Install from a local source directory
+
+If you have downloaded or cloned this package locally, enter the package directory and install it with:
+
+```bash
+cd tetss_rampage_package
+pip install -e .
+```
+
+After installation, check whether the command-line tool is available:
+
+```bash
+tetss2 --help
+```
+
+### Option 2: Recommended conda environment
+
+We recommend creating a clean conda environment before installation:
+
+```bash
+
+conda create -n tetss2 python=3.9
+conda activate tetss2
+conda install numpy pandas scikit-learn
+pip install torch==1.10.2
+
+pip install -e .
+
+```
+
+A future public release may support:
+
+```bash
+pip install tetss2
+```
+
+---
+
+## Command-line usage
+
+### 1. Predict a single sequence
+
+```bash
+tetss2 predict --sequence ACGTACGTACGTACGT
+```
+
+For normal use, the input sequence should be exactly 201 bp:
+
+```bash
+tetss2 predict --sequence YOUR_201BP_DNA_SEQUENCE
+```
+
+Example output:
+
+```json
+{
+  "model": "TETSS2.0",
+  "sequence": "ACGTACGTACGTACGT",
+  "sequence_length": 16,
+  "probability": 0.35490313172340393,
+  "prediction": 0,
+  "threshold": 0.5
+}
+```
+
+Note: the example above uses a short sequence only to demonstrate the command format. For biological prediction, please use a 201 bp sequence.
+
+---
+
+### 2. Batch prediction from a TSV file
+
+Prepare an input file containing a `sequence` column.
+
+Example input file: `input.tsv`
+
+```tsv
+sample_id	sequence
+sample1	ACGT...
+sample2	TTTT...
+sample3	GCGC...
+```
+
+Run batch prediction:
+
+```bash
+tetss2 predict-file \
+  --input input.tsv \
+  --output tetss2_predictions.tsv
+```
+
+The output file will contain the original columns plus TETSS2.0 prediction results.
+
+Example output:
+
+```tsv
+sample_id	sequence	tetss2_sequence_length	tetss2_probability	tetss2_prediction	tetss2_threshold
+sample1	ACGT...	201	0.3549	0	0.5
+sample2	TTTT...	201	0.8123	1	0.5
+sample3	GCGC...	201	0.4471	0	0.5
+```
+
+---
+
+### 3. Batch prediction from a CSV file
+
+If your input file is comma-separated, use `--sep ","`:
+
+```bash
+tetss2 predict-file \
+  --input input.csv \
+  --output tetss2_predictions.csv \
+  --sep ","
+```
+
+---
+
+### 4. Use a custom sequence column name
+
+If the sequence column is not named `sequence`, specify it with `--sequence-column`.
+
+For example, if the input file contains a column named `dna`:
+
+```bash
+tetss2 predict-file \
+  --input input.tsv \
+  --output tetss2_predictions.tsv \
+  --sequence-column dna
+```
+
+---
+
+## Python API usage
+
+TETSS2.0 can also be used directly in Python.
+
+```python
+from tetss2 import TETSS2Predictor
+
+predictor = TETSS2Predictor()
+
+result = predictor.predict("YOUR_201BP_DNA_SEQUENCE")
+print(result)
+```
+
+Example output:
+
+```python
+{
+    "model": "TETSS2.0",
+    "sequence": "YOUR_201BP_DNA_SEQUENCE",
+    "sequence_length": 201,
+    "probability": 0.73,
+    "prediction": 1,
+    "threshold": 0.5,
+}
+```
+
+---
+
+## Model architecture
+
+TETSS2.0 uses a one-dimensional convolutional neural network for DNA sequence classification.
+
+The model contains:
+
+* one-hot encoding of DNA sequences
+* multiple 1D convolutional layers
+* batch normalization
+* ReLU activation
+* max pooling
+* adaptive max pooling
+* fully connected classification layers
+
+The model outputs a single logit, which is converted to a probability using the sigmoid function.
+
+---
+
+## Model files
+
+The package includes the trained model weight file:
+
+```text
+best_model.pth
+```
+
+The original training output directory also contains:
+
+```text
+best_model.pth
+run_config.json
+train_history.tsv
+final_val_metrics.json
+split_summary.json
+train_split.tsv
+val_split.tsv
+```
+
+These files can be used to document model configuration, validation performance, and data splitting information.
+
+---
+
+## Validation performance
+
+Please fill in the following values using `final_val_metrics.json`:
+
+| Metric          | Value |
+| --------------- | ----: |
+| AUROC           |  TODO |
+| AUPRC           |  TODO |
+| Accuracy        |  TODO |
+| Precision       |  TODO |
+| Recall          |  TODO |
+| True negatives  |  TODO |
+| False positives |  TODO |
+| False negatives |  TODO |
+| True positives  |  TODO |
+
+To view the metrics file:
+
+```bash
+cat final_val_metrics.json
+```
+
+---
+
+## Troubleshooting
+
+### MKL threading error
+
+If you see an error similar to:
+
+```text
+mkl-service + Intel(R) MKL: MKL_THREADING_LAYER=INTEL is incompatible with libgomp.so.1
+```
+
+try running:
+
+```bash
+export MKL_THREADING_LAYER=GNU
+```
+
+Then run the prediction command again.
+
+---
+
+### Cannot find sequence column
+
+If you see an error like:
+
+```text
+Cannot find sequence column 'sequence'
+```
+
+check whether your input file contains a real tab or comma separator.
+
+For a TSV file, you can check tabs with:
+
+```bash
+cat -A input.tsv
+```
+
+A real tab will appear as:
+
+```text
+^I
+```
+
+A correct TSV file should look like:
+
+```text
+sample_id^Isequence$
+sample1^IACGT...$
+```
+
+---
+
+## Citation
+
+If you use TETSS2 in your research, please cite:
+
+@software{tetss2,
+  title={TETSS2: Deep Learning Model for TE-TSS Prediction},
+  year={2026}
+}
+
+---
+
+## Contact
+
+For questions or issues, please contact the developer or open an issue in the project repository.
+
+---
+
+## License
+
+License information will be added later.
+
+## Repository
+
+https://github.com/MoriyaaCui/TETSS2.git
+
+
+## Live Demo
+
+A Gradio demo is available:
+
+```bash
+python demo/app.py

tetss2-0.1.0/README.md

@@ -0,0 +1,364 @@
+# TETSS2.0
+
+**TETSS2.0** is a deep learning model for predicting TE-derived transcription start site (TE-TSS) activity from DNA sequences.
+
+The Python package name and command-line tool name are **`tetss2`**. The model name shown in documents, figures, and the website is **TETSS2.0**.
+
+---
+
+## Overview
+
+TETSS2.0 is a PyTorch-based convolutional neural network classifier designed to predict whether an input DNA sequence is associated with TE-TSS activity.
+
+The model takes a DNA sequence as input and returns:
+
+* a prediction probability
+* a binary prediction label
+* the classification threshold used for prediction
+
+By default, TETSS2.0 uses a threshold of `0.5`.
+
+---
+
+## Input requirement
+
+TETSS2.0 expects DNA sequences of exactly **201 bp**.
+
+Allowed bases:
+
+```text
+A, C, G, T, N
+```
+
+Notes:
+
+* Input sequences are automatically converted to uppercase.
+* `N` is allowed but is encoded as an all-zero position in the one-hot representation.
+* Sequences shorter or longer than 201 bp are rejected by default.
+* The option `--no-length-check` is available only for debugging and is not recommended for normal prediction.
+
+---
+
+## Output
+
+For each input sequence, TETSS2.0 outputs:
+
+| Column                   | Description                              |
+| ------------------------ | ---------------------------------------- |
+| `tetss2_sequence_length` | Length of the input sequence             |
+| `tetss2_probability`     | Predicted probability score              |
+| `tetss2_prediction`      | Binary prediction result, `0` or `1`     |
+| `tetss2_threshold`       | Threshold used for binary classification |
+
+---
+
+## Installation
+
+### Option 1: Install from a local source directory
+
+If you have downloaded or cloned this package locally, enter the package directory and install it with:
+
+```bash
+cd tetss_rampage_package
+pip install -e .
+```
+
+After installation, check whether the command-line tool is available:
+
+```bash
+tetss2 --help
+```
+
+### Option 2: Recommended conda environment
+
+We recommend creating a clean conda environment before installation:
+
+```bash
+
+conda create -n tetss2 python=3.9
+conda activate tetss2
+conda install numpy pandas scikit-learn
+pip install torch==1.10.2
+
+pip install -e .
+
+```
+
+A future public release may support:
+
+```bash
+pip install tetss2
+```
+
+---
+
+## Command-line usage
+
+### 1. Predict a single sequence
+
+```bash
+tetss2 predict --sequence ACGTACGTACGTACGT
+```
+
+For normal use, the input sequence should be exactly 201 bp:
+
+```bash
+tetss2 predict --sequence YOUR_201BP_DNA_SEQUENCE
+```
+
+Example output:
+
+```json
+{
+  "model": "TETSS2.0",
+  "sequence": "ACGTACGTACGTACGT",
+  "sequence_length": 16,
+  "probability": 0.35490313172340393,
+  "prediction": 0,
+  "threshold": 0.5
+}
+```
+
+Note: the example above uses a short sequence only to demonstrate the command format. For biological prediction, please use a 201 bp sequence.
+
+---
+
+### 2. Batch prediction from a TSV file
+
+Prepare an input file containing a `sequence` column.
+
+Example input file: `input.tsv`
+
+```tsv
+sample_id	sequence
+sample1	ACGT...
+sample2	TTTT...
+sample3	GCGC...
+```
+
+Run batch prediction:
+
+```bash
+tetss2 predict-file \
+  --input input.tsv \
+  --output tetss2_predictions.tsv
+```
+
+The output file will contain the original columns plus TETSS2.0 prediction results.
+
+Example output:
+
+```tsv
+sample_id	sequence	tetss2_sequence_length	tetss2_probability	tetss2_prediction	tetss2_threshold
+sample1	ACGT...	201	0.3549	0	0.5
+sample2	TTTT...	201	0.8123	1	0.5
+sample3	GCGC...	201	0.4471	0	0.5
+```
+
+---
+
+### 3. Batch prediction from a CSV file
+
+If your input file is comma-separated, use `--sep ","`:
+
+```bash
+tetss2 predict-file \
+  --input input.csv \
+  --output tetss2_predictions.csv \
+  --sep ","
+```
+
+---
+
+### 4. Use a custom sequence column name
+
+If the sequence column is not named `sequence`, specify it with `--sequence-column`.
+
+For example, if the input file contains a column named `dna`:
+
+```bash
+tetss2 predict-file \
+  --input input.tsv \
+  --output tetss2_predictions.tsv \
+  --sequence-column dna
+```
+
+---
+
+## Python API usage
+
+TETSS2.0 can also be used directly in Python.
+
+```python
+from tetss2 import TETSS2Predictor
+
+predictor = TETSS2Predictor()
+
+result = predictor.predict("YOUR_201BP_DNA_SEQUENCE")
+print(result)
+```
+
+Example output:
+
+```python
+{
+    "model": "TETSS2.0",
+    "sequence": "YOUR_201BP_DNA_SEQUENCE",
+    "sequence_length": 201,
+    "probability": 0.73,
+    "prediction": 1,
+    "threshold": 0.5,
+}
+```
+
+---
+
+## Model architecture
+
+TETSS2.0 uses a one-dimensional convolutional neural network for DNA sequence classification.
+
+The model contains:
+
+* one-hot encoding of DNA sequences
+* multiple 1D convolutional layers
+* batch normalization
+* ReLU activation
+* max pooling
+* adaptive max pooling
+* fully connected classification layers
+
+The model outputs a single logit, which is converted to a probability using the sigmoid function.
+
+---
+
+## Model files
+
+The package includes the trained model weight file:
+
+```text
+best_model.pth
+```
+
+The original training output directory also contains:
+
+```text
+best_model.pth
+run_config.json
+train_history.tsv
+final_val_metrics.json
+split_summary.json
+train_split.tsv
+val_split.tsv
+```
+
+These files can be used to document model configuration, validation performance, and data splitting information.
+
+---
+
+## Validation performance
+
+Please fill in the following values using `final_val_metrics.json`:
+
+| Metric          | Value |
+| --------------- | ----: |
+| AUROC           |  TODO |
+| AUPRC           |  TODO |
+| Accuracy        |  TODO |
+| Precision       |  TODO |
+| Recall          |  TODO |
+| True negatives  |  TODO |
+| False positives |  TODO |
+| False negatives |  TODO |
+| True positives  |  TODO |
+
+To view the metrics file:
+
+```bash
+cat final_val_metrics.json
+```
+
+---
+
+## Troubleshooting
+
+### MKL threading error
+
+If you see an error similar to:
+
+```text
+mkl-service + Intel(R) MKL: MKL_THREADING_LAYER=INTEL is incompatible with libgomp.so.1
+```
+
+try running:
+
+```bash
+export MKL_THREADING_LAYER=GNU
+```
+
+Then run the prediction command again.
+
+---
+
+### Cannot find sequence column
+
+If you see an error like:
+
+```text
+Cannot find sequence column 'sequence'
+```
+
+check whether your input file contains a real tab or comma separator.
+
+For a TSV file, you can check tabs with:
+
+```bash
+cat -A input.tsv
+```
+
+A real tab will appear as:
+
+```text
+^I
+```
+
+A correct TSV file should look like:
+
+```text
+sample_id^Isequence$
+sample1^IACGT...$
+```
+
+---
+
+## Citation
+
+If you use TETSS2 in your research, please cite:
+
+@software{tetss2,
+  title={TETSS2: Deep Learning Model for TE-TSS Prediction},
+  year={2026}
+}
+
+---
+
+## Contact
+
+For questions or issues, please contact the developer or open an issue in the project repository.
+
+---
+
+## License
+
+License information will be added later.
+
+## Repository
+
+https://github.com/MoriyaaCui/TETSS2.git
+
+
+## Live Demo
+
+A Gradio demo is available:
+
+```bash
+python demo/app.py