[ENH] Add from_dataframe factory method to APIDataset

Implemented a class method from_dataframe() in APIDataset to facilitate
dataset creation directly from pandas DataFrames. This is highly useful
as many users store interaction data in tabular formats.

Features:
- Convenience method for pandas integration
- Automatic extraction of columns to numpy arrays
- Included comprehensive test suite for APIDataset

Author: Vaishnav88sk

pyaptamer/datasets/dataclasses/_api.py

@@ -2,6 +2,7 @@
 __all__ = ["APIDataset"]
 
 import numpy as np
+import pandas as pd
 import torch
 from torch.utils.data import Dataset
 
@@ -58,6 +59,58 @@ def __init__(
 
         self.len = len(self.x_apta)
 
+    @classmethod
+    def from_dataframe(
+        cls,
+        df: pd.DataFrame,
+        apta_col: str,
+        prot_col: str,
+        label_col: str,
+        apta_max_len: int,
+        prot_max_len: int,
+        prot_words: dict[str, int],
+        split: str = "train",
+    ) -> "APIDataset":
+        """
+        Create an APIDataset from a pandas DataFrame.
+
+        Parameters
+        ----------
+        df : pd.DataFrame
+            The dataframe containing the data.
+        apta_col : str
+            The name of the column containing aptamer sequences.
+        prot_col : str
+            The name of the column containing protein sequences.
+        label_col : str
+            The name of the column containing interaction labels.
+        apta_max_len : int
+            Maximum length for aptamer sequences.
+        prot_max_len : int
+            Maximum length for protein sequences.
+        prot_words : dict[str, int]
+            Protein k-mer word mapping.
+        split : str, optional, default="train"
+            If "train", the dataset will augment aptamer sequences.
+
+        Returns
+        -------
+        APIDataset
+            An instance of APIDataset.
+        """
+        x_apta = df[apta_col].values
+        x_prot = df[prot_col].values
+        y = df[label_col].values
+        return cls(
+            x_apta=x_apta,
+            x_prot=x_prot,
+            y=y,
+            apta_max_len=apta_max_len,
+            prot_max_len=prot_max_len,
+            prot_words=prot_words,
+            split=split,
+        )
+
     def _prepare_data(
         self,
         x_apta: np.ndarray,

pyaptamer/datasets/tests/test_api_dataset.py

@@ -0,0 +1,80 @@
+"""Tests for APIDataset class."""
+
+import numpy as np
+import pandas as pd
+import pytest
+import torch
+
+from pyaptamer.datasets.dataclasses import APIDataset
+
+
+class TestAPIDataset:
+    """Tests for APIDataset."""
+
+    @pytest.fixture
+    def dummy_data(self):
+        apta = np.array(["AUGC", "GCAU"])
+        prot = np.array(["ACD", "EFG"])
+        y = np.array(["positive", "negative"])
+        words = {"ACD": 1, "EFG": 2}
+        return apta, prot, y, words
+
+    def test_init_train(self, dummy_data):
+        """Test initialization with train split (augmentation)."""
+        apta, prot, y, words = dummy_data
+        ds = APIDataset(
+            x_apta=apta,
+            x_prot=prot,
+            y=y,
+            apta_max_len=10,
+            prot_max_len=10,
+            prot_words=words,
+            split="train",
+        )
+        # Augmentation (reverse) doubles the size
+        assert len(ds) == 4
+        assert isinstance(ds[0][0], torch.Tensor)
+        assert isinstance(ds[0][1], torch.Tensor)
+        assert isinstance(ds[0][2], torch.Tensor)
+
+    def test_init_test(self, dummy_data):
+        """Test initialization with test split (no augmentation)."""
+        apta, prot, y, words = dummy_data
+        ds = APIDataset(
+            x_apta=apta,
+            x_prot=prot,
+            y=y,
+            apta_max_len=10,
+            prot_max_len=10,
+            prot_words=words,
+            split="test",
+        )
+        assert len(ds) == 2
+
+    def test_from_dataframe(self, dummy_data):
+        """Test from_dataframe factory method."""
+        apta, prot, y, words = dummy_data
+        df = pd.DataFrame({"apta": apta, "prot": prot, "label": y})
+        
+        ds = APIDataset.from_dataframe(
+            df=df,
+            apta_col="apta",
+            prot_col="prot",
+            label_col="label",
+            apta_max_len=10,
+            prot_max_len=10,
+            prot_words=words,
+            split="test",
+        )
+        
+        assert len(ds) == 2
+        # Check that data was correctly passed
+        # Label 'positive' becomes 1, 'negative' becomes 0
+        assert ds[0][2].item() == 1
+        assert ds[1][2].item() == 0
+
+    def test_invalid_split(self, dummy_data):
+        """Test that invalid split raises ValueError."""
+        apta, prot, y, words = dummy_data
+        with pytest.raises(ValueError, match="Unknown split"):
+            APIDataset(apta, prot, y, 10, 10, words, split="val")