adding few functions for right and left legs collision

.gitignore

@@ -41,3 +41,4 @@ dist/
 *.backup
 looplib.egg-info/*
 .ipynb_checkpoints/*
+.ipynb_checkpoints/

looplib/barriertools.py

@@ -0,0 +1,77 @@
+def peak_positions(boundary_list, window_sizes=[1]):
+    """
+    Calculate peak positions based on a boundary_list within window_sizes.
+
+    Args:
+        boundary_list (list): List of boundary values.
+        window_sizes (list, optional): List of window sizes. Defaults to [1].
+
+    Returns:
+        np.ndarray: Array containing peak positions.
+    """
+    peak_monomers = np.array([])
+
+    for i in window_sizes:
+        inds_to_add = [boundary + i for boundary in boundary_list]
+        peak_monomers = np.hstack((peak_monomers, inds_to_add))
+
+    return peak_monomers.astype(int)
+
+
+def FRiP(num_sites_t, lef_positions, peak_positions):
+    """
+    Calculate the Fraction of Reads in Peaks (FRiP) score.
+
+    The FRiP score is a measure of how many loop-extruding factor (LEF) positions 
+    fall within predefined peak regions, relative to the total number of LEF positions.
+
+    Parameters:
+    -----------
+    num_sites_t : int
+        Total number of genomic sites.
+    lef_positions : array-like
+        Positions of loop extruding factors (LEFs) along the genome.
+    peak_positions : array-like
+        Indices corresponding to peak regions (CTCFs).
+
+    Returns:
+    --------
+    float
+        The fraction of LEF positions that fall within peak regions.
+    """
+    hist, edges = np.histogram(lef_positions, np.arange(num_sites_t + 1))
+    return np.sum(hist[peak_positions]) / len(lef_positions)
+
+
+def find_convergent_pairs(ctcf_right, ctcf_left, elements_between_pairs):
+    """
+    Finds pairs of convergent CTCF binding sites with exactly `elements_between_pairs` barrier elements between them.
+
+    Parameters:
+    ----------
+    ctcf_right : list of int
+        List of positions for CTCF binding sites on the right (right-facing CTCF sites).
+    ctcf_left : list of int
+        List of positions for CTCF binding sites on the left (left-facing CTCF sites).
+    elements_between_pairs : int
+        The number of barrier elements between the convergent CTCF pairs. 
+        For example, `elements_between_pairs=1` finds directly connected CTCF sites, 
+        `elements_between_pairs=2` finds CTCF sites with one intervening barrier element between them, etc.
+
+    Returns:
+    -------
+    list of list of int
+        A list of pairs of convergent CTCF sites, where each pair consists of one 
+        left-facing CTCF site and one right-facing CTCF site, separated by exactly `elements_between_pairs` barriers.
+    """
+    # Combine and sort CTCF positions from both directions
+    ctot = np.sort(np.array(ctcf_right + ctcf_left))
+
+    # Find pairs of convergent CTCF elements with exactly `elements_between_pairs` barriers between them
+    convergent_pairs = [
+        [ctot[i], ctot[i + elements_between_pairs]] 
+        for i in range(len(ctot) - elements_between_pairs) 
+        if ctot[i] in ctcf_left and ctot[i + elements_between_pairs] in ctcf_right
+    ]
+
+    return convergent_pairs