evaluate.py 24.8 KB
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#!/usr/bin/env python3


import sys
import argparse
from termcolor import colored
import networkx as nx
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sys.setrecursionlimit(10000)
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def parse_args():
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    parser = argparse.ArgumentParser(description='Process a d2 graph (complete graph or path) to evaluate its quality.')
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    parser.add_argument('filename', type=str,
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                        help='The file to evalute')
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    parser.add_argument('--type', '-t', choices=["d2", "path", "d2-2annotate", "dgraphs"], default="path", required=True,
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                        help="Define the data type to evaluate. Must be 'd2' or 'path' or 'd2-2annotate' (Rayan's hack).")
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    parser.add_argument('--light-print', '-l', action='store_true',
                        help='Print only wrong nodes and paths')
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    parser.add_argument('--max_gap', '-g', type=int, default=0, help="Allow to jump over max_gap nodes during the increasing path search")
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    parser.add_argument('--barcode_graph', '-b', help="Path to the barcode graph corresponding to the d2_graph to analyse.")
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    parser.add_argument('--optimization_file', '-o',
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                        help="If the main file is a d2, a file formatted for optimization can be set. This file will be used to compute the coverage of the longest path on the barcode graph.")
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    args = parser.parse_args()
    return args


def load_graph(filename):
    if filename.endswith('.graphml'):
        return nx.read_graphml(filename)
    elif filename.endswith('.gexf'):
        return nx.read_gexf(filename)
    else:
        print("Wrong file format. Require graphml or gefx format", file=sys.stderr)
        exit()

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def save_graph(g, filename):
    if filename.endswith('.graphml'):
        return nx.write_graphml(g,filename)
    elif filename.endswith('.gexf'):
        return nx.write_gexf(g,filename)
    else:
        print("Wrong file format. Require graphml or gefx format", file=sys.stderr)
        exit()

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def transform_bg(graph):
    idx = 0
    node_names = {}
    nx.set_node_attributes(graph, 0, 'score')
    nx.set_node_attributes(graph, "", 'barcode_edges')
    for node in graph.nodes():
        graph.nodes[node]['udg'] = f"[{node}][][]"
        node_names[node] = str(idx)
        idx += 1

    graph = nx.relabel_nodes(graph, node_names)

    return graph

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# ------------- Path Graph -------------

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def mols_from_node(node_name):
    return [int(idx) for idx in node_name.split(":")[1].split(".")[0].split("_")]


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def parse_udg_qualities(graph):
    """ Compute the quality for the best udgs present in the graph.
        All the node names must be under the format :
        {idx}:{mol1_id}_{mol2_id}_...{molx_id}.other_things_here
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        :param graph: The networkx graph representing the deconvolved graph
        :return: A tuple containing two dictionaries. The first one with theoretical frequencies of each node, the second one with observed frequencies.
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    """
    dg_per_node = {}

    for node, data in graph.nodes(data=True):
        str_udg = data["udg"]
        central, h1, h2 = str_to_udg_lists(str_udg)

        if central not in dg_per_node:
            dg_per_node[central] = []
        dg_per_node[central].append(data["udg"])

    for node in dg_per_node:
        print(node, dg_per_node[node])
        print(len(dg_per_node))

    return dg_per_node


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def parse_path_graph_frequencies(graph, barcode_graph):
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    """ Compute appearance frequencies from node names.
        All the node names must be under the format :
        {idx}:{mol1_id}_{mol2_id}_...{molx_id}.other_things_here
        :param graph: The networkx graph representing the deconvolved graph
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        :param barcode_graph: The barcode graph
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        :return: A tuple containing two dictionaries. The first one with theoretical frequencies of each node, the second one with observed frequencies.
    """
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    # Compute origin nodes formatted as `{idx}:{mol1_id}_{mol2_id}_...`
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    observed_frequencies = {}
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    real_frequencies = {}
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    origin_node_names = []
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    node_per_barcode = {}

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    for node, data in graph.nodes(data=True):
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        parsed = parse_dg_name(graph, node)
        origin_name = parsed[0][1]
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        if origin_name not in node_per_barcode:
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            node_per_barcode[origin_name] = []
        node_per_barcode[origin_name].append(node)
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        # Count frequency
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        if origin_name not in observed_frequencies:
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            observed_frequencies[origin_name] = 0
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            origin_node_names.append(origin_name)
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        observed_frequencies[origin_name] += 1
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    # Theoretical frequencies
    real_frequencies = {node_id: len(node_id.split(":")[1].split("_")) for node_id in barcode_graph.nodes()}
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    return real_frequencies, observed_frequencies, node_per_barcode
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def parse_graph_path(graph):
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    """ This function aims to look for direct molecule neighbors.
        If a node has more than 2 direct neighbors, it's not rightly split
    """
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    neighborhood = {}

    for node in graph.nodes():
        molecules = mols_from_node(node)
        neighbors = list(graph.neighbors(node))
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        neighborhood[node] = []
        for mol in molecules:
            for nei in neighbors:
                nei_mols = mols_from_node(nei)
                if mol-1 in nei_mols:
                    neighborhood[node].append(nei)
                if mol+1 in nei_mols:
                    neighborhood[node].append(nei)
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    return neighborhood
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def print_path_summary(frequencies, light_print=False, file_pointer=sys.stdout):
    if file_pointer is None:
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        return

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    print("--- Nodes analysis ---", file=file_pointer)
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    theoretical_frequencies, observed_frequencies, node_per_barcode = frequencies
    for key in theoretical_frequencies:
        obs, the = observed_frequencies[key] if key in observed_frequencies else 0, theoretical_frequencies[key]
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        result = f"{key}: {obs}/{the}"

        if file_pointer == sys.stdout:
            result = colored(result, 'green' if obs==the else 'red')

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        if light_print and obs == the:
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            continue

        print(result, file=file_pointer)


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    print("--- Global summary ---", file=file_pointer)

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    # --- Frequency usage ---
    # Tags
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    distinct_theoretical_nodes = len(theoretical_frequencies)
    distinct_observed_nodes = len(observed_frequencies)
    print(f"Distinct barcodes: {distinct_observed_nodes}/{distinct_theoretical_nodes}", file=file_pointer)
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    # molecules
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    cumulative_theoretical_nodes = sum(theoretical_frequencies.values())
    cumulative_observed_nodes = sum(observed_frequencies.values())
    print(f"Molecules: {cumulative_observed_nodes}/{cumulative_theoretical_nodes}", file=file_pointer)
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    # Wrong splits
    over_split = 0
    under_split = 0
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    for barcode in theoretical_frequencies:
        observed = observed_frequencies[barcode] if barcode in observed_frequencies else 0
        theoretic = theoretical_frequencies[barcode]
        over_split += max(observed-theoretic, 0)
        under_split += max(theoretic-observed, 0)
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    print(f"Under/Over splitting: {under_split} - {over_split}")
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def print_dgraphs_summary(frequencies, light_print=False):
    pass


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# ------------- D2 Graph -------------

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def str_to_udg_lists(s):
    udg = s.replace("]", "").replace(' [', '[')
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    return udg.split('[')[1:]
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# speeds up networkx access to attributes
cached_udg_attr = None
cached_score_attr = None

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def parse_dg_name(gr, name):
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    global cached_udg_attr, cached_score_attr 
    if cached_udg_attr is None:
        cached_udg_attr = nx.get_node_attributes(gr, 'udg')
    udg = cached_udg_attr[name]
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    res = str_to_udg_lists(udg)
    if len(res) != 3:
        print("parsing problem:",res)
    central, h1, h2 = res
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    idx = name
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    if cached_score_attr is None:
        cached_score_attr = nx.get_node_attributes(gr, 'score')
    score = cached_score_attr[name]
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    # Parse hands
    h1 = h1.split(', ')
    h2 = h2.split(', ')

    return (idx, central, score), h1, h2


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def path_to_jumps(path):
    chuncks = []
    prev_start = -1000
    current_molecule = -1000

    for mol, node in path:
        # If there is a gap
        if mol > current_molecule + 1:
            chuncks.append((prev_start, current_molecule))
            prev_start = mol

        current_molecule = mol

    # Add the last piece
    chuncks.append((prev_start, current_molecule))

    del chuncks[0]
    return chuncks


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def print_d2_summary(connected_components, longest_path, coverage_vars=(0, 0), light_print=False):
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    print("--- Global summary ---")
    print(f"Number of connected components: {len(connected_components)}")
    print(f"Total number of nodes: {sum([len(x) for x in connected_components])}")
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    no_singleton = [x for x in connected_components if len(x) > 1]
    print(f"There are {len(no_singleton)} connex components with at least 2 nodes")
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    print(f"The 5 largest components: {[len(x) for x in connected_components][:5]}")

    print("--- Largest component analysis ---")
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    # Get the list of node idx
    path_dg_idx = [int(x[1].split(" ")[0]) for x in longest_path]
    # print("\n".join(longest_path))
    if not light_print:
        print("Longest path for increasing molecule number:")
        print(path_dg_idx)
    print(f"Size of the longest path: {len(longest_path)}")
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    if not light_print:
        print("Jumps in central nodes:")
        print(path_to_jumps(longest_path))
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    print(f"Number of usable coverage variables: {len(coverage_vars[1])}")
    print(f"Coverage: {len(coverage_vars[0])}/{len(coverage_vars[1])}")
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    if not light_print:
        print(f"Missing coverage variables:\n{coverage_vars[1]-coverage_vars[0]}")

def _get_distant_neighbors(graph, node, dist):
    neighbors = set()

    to_compute = [node]
    for _ in range(dist):
        next_compute = []
        for node in to_compute:
            for neighbor in graph[node]:
                if neighbor not in neighbors:
                    neighbors.add(neighbor)
                    next_compute.append(neighbor)
        to_compute = next_compute
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    return neighbors
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def compute_next_nodes(d2_component, max_jumps=0):
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    # First parse dg names
    dg_names = {}
    for node in d2_component.nodes():
        dg_names[node] = parse_dg_name(d2_component,node)

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    next_nodes = {}

    for node in d2_component.nodes():
        # Parse the current node name
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        head, h1, h2 = dg_names[node]
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        next_nodes[node] = {}

        # Get the current molecule idxs
        molecule_idxs = mols_from_node(head[1])
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        #print("node",node,"dg name",dg_names[node],"mol idxs",molecule_idxs)

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        for mol_idx in molecule_idxs:
            nexts = []
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            # for neighbor in d2_component[node]:
            for neighbor in _get_distant_neighbors(d2_component, node, max_jumps+1):
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                # nei_head: central node of the neighbor of 'node'
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                nei_head, _, _ = dg_names[neighbor]
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                nei_mols = mols_from_node(nei_head[1])
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                # only consider neighbor molecules that are strictly bigger than the current molecule idx considered (from 'node')
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                nei_mols = [x for x in nei_mols if x > mol_idx]
                
                # If there are molecule next
                if len(nei_mols) > 0:
                    next_nei_mol = min(nei_mols)
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                    # append to the neighbors of (node,mol_idx) that 'neighbor' if it contains a molecule that's bigger than mol_idx
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                    nexts.append((next_nei_mol, neighbor))

            nexts.sort(key=lambda x: x[0])
            next_nodes[node][mol_idx] = nexts
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            # print("next nodes of node",node,"mol idx",mol_idx,":",next_nodes)
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    return next_nodes


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def compute_longest_increasing_paths(d2_component, max_gap=0):
    next_nodes = compute_next_nodes(d2_component, max_jumps=max_gap)
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    sys.setrecursionlimit(len(d2_component.nodes)*2)
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    # Compute the longest path for each node
    longest_paths = {}
    for idx, start_node in enumerate(next_nodes):
        # print(f"{idx}/{len(next_nodes)}")
        for mol_idx in next_nodes[start_node]:
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            recursive_longest_path(start_node, mol_idx, next_nodes, longest_paths)
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    # Get the longest path size,
    # across all barcode graph nodes and all molecules in these barcodes
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    max_len, node_val, mol_idx = 0, None, -1
    for node in longest_paths:
        for mol in longest_paths[node]:
            length, _, _ = longest_paths[node][mol]
            if max_len < length:
                max_len = length
                node_val = node
                mol_idx = mol

    # Backtrack the longest path
    path = backtrack_longest_path(node_val, mol_idx, longest_paths)
    return path


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def compute_shortest_edit_path(path):
    min_mol = float("inf")
    max_mol = 0
    molecules = {}

    path_extremes = []
    node_names = {}

    # Parse molecules
    for node_name, data in path.nodes(data=True):
        udg = data["udg"]
        central_node = udg.split(']')[0][1:]

        node_names[node_name] = central_node
        if len(list(path[node_name])) == 1:
            path_extremes.append(node_name)

        mol_names = central_node.split(":")[1].split('_')
        for mol_name in mol_names:
            mol_idx = int(mol_name)
            if mol_idx < min_mol: min_mol = mol_idx
            if mol_idx >= max_mol: max_mol = mol_idx
            molecules[mol_idx] = central_node

    # create barcode path from molecules
    molecule_order = []
    for idx in range(min_mol, max_mol+1):
        if idx in molecules:
            molecule_order.append(molecules[idx])

    # create barcode path from d2_path
    first = path_extremes[0]
    last = path_extremes[1]
    d2_path_order = [first, list(path[first])[0]]
    while d2_path_order[-1] != last:
        neighbors = list(path[d2_path_order[-1]])

        if neighbors[0] == d2_path_order[-2]:
            d2_path_order.append(neighbors[1])
        else:
            d2_path_order.append(neighbors[0])
    d2_path_order = [node_names[x] for x in d2_path_order]

    edit_path = edit_distance(molecule_order, d2_path_order)
    filtered_edit_path = [x[0] for x in edit_path if x[0] == x[1]]
    reverse_edit_path = edit_distance(molecule_order, d2_path_order[::-1])
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    reverse_filtered_edit_path = [x[0] for x in reverse_edit_path if x[0] == x[1]]
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    if len(filtered_edit_path) > len(reverse_filtered_edit_path):
        return filtered_edit_path
    else:
        return reverse_filtered_edit_path



def edit_distance(array_vertical, array_horizontal):
    dynamic = [[float("inf") for column in range(len(array_horizontal)+1)] for row in range(len(array_vertical)+1)]
    # Fill init line and column
    for i in range(len(array_horizontal)+1):
        dynamic[0][i] = i
    for i in range(len(array_vertical)+1):
        dynamic[i][0] = i

    # Fill the array
    for row in range(1, len(array_vertical)+1):
        for column in range(1, len(array_horizontal)+1):
            if array_vertical[row-1] == array_horizontal[column-1]:
                dynamic[row][column] = min(dynamic[row-1][column-1], dynamic[row-1][column]+1, dynamic[row][column-1]+1)
            else:
                dynamic[row][column] = min(dynamic[row-1][column-1]+1, dynamic[row-1][column]+1, dynamic[row][column-1]+1)

    # Compute alignment
    row = len(array_vertical)
    column = len(array_horizontal)
    path = [(array_vertical[row-1], array_horizontal[column-1])]

    while row != 0 and column != 0:
        score = dynamic[row][column]
        # Match
        if array_vertical[row-1] == array_horizontal[column-1] and dynamic[row-1][column-1] == dynamic[row][column]:
            row -= 1
            column -= 1
        elif array_vertical[row-1] != array_horizontal[column-1] and dynamic[row-1][column-1] == dynamic[row][column] - 1:
            row -= 1
            column -= 1
        elif dynamic[row-1][column] == dynamic[row][column] - 1:
            row -= 1
        elif dynamic[row][column-1] == dynamic[row][column] - 1:
            column -= 1
        else:
            print("Huge problem in edit distance !", file=sys.stderr)
            return []

        path.append((array_vertical[row-1], array_horizontal[column-1]))

    for finalize_row in range(row-1, -1, -1):
        path.append((array_vertical[finalize_row], array_horizontal[column]))
    for finalize_column in range(column-1, -1, -1):
        path.append((array_vertical[row], array_horizontal[finalize_column]))

    return path[::-1]


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def backtrack_longest_path(node, molecule, longest_paths, path=[]):
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    if node is None:
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        return path

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    path.append((molecule, node))
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    length, next_node, next_mol = longest_paths[node][molecule]
    return backtrack_longest_path(next_node, next_mol, longest_paths, path)


def recursive_longest_path(current_node, current_molecule, next_nodes, longest_paths):
    # Dynamic programming
    if current_node in longest_paths and current_molecule in longest_paths[current_node]:
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        #print("getting cached result for node",current_node,"mol",current_molecule,longest_paths[current_node][current_molecule])
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        return longest_paths[current_node][current_molecule]

    longest = 0
    longest_next = None
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    min_mol_idx = float('inf') 
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    # Recursively compute the longest path
    for mol_idx, node in next_nodes[current_node][current_molecule]:
        size, _, _ = recursive_longest_path(node, mol_idx, next_nodes, longest_paths)
        if size + 1 > longest:
            longest = size + 1
            longest_next = node
            min_mol_idx = mol_idx
        # If there is an alternative path with shorter distance
        elif size + 1 == longest and mol_idx < min_mol_idx:
            longest = size + 1
            longest_next = node
            min_mol_idx = mol_idx
    
    # Save the result
    if not current_node in longest_paths:
        longest_paths[current_node] = {}
    longest_paths[current_node][current_molecule] = (longest, longest_next, min_mol_idx)
    return longest_paths[current_node][current_molecule]


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def compute_covered_variables(graph, path):
    path_nodes = set()
    for mol, node_name in path:
        path_nodes.add(node_name)
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    used_vars = set()
    total_vars = set()
    for node, data in graph.nodes(data=True):
        vars = data["barcode_edges"].split(" ")
        total_vars.update(vars)
        if node in path_nodes:
            used_vars.update(vars)
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    return used_vars, total_vars
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# returns True iff there exist x in mol1 such that there exists y in mol2 and |x-y| <= some_value
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def nearby_udg_molecules(mols1, mols2):
    for x in mols1:
        for y in mols2:
            if abs(x-y) <= 5:
                return True
    return False

def verify_graph_edges(d2_component):
    udg_molecules_dict=dict()
    for node in d2_component.nodes():
        # Parse the current node name
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        head, c1, c2 = parse_dg_name(d2_component,node)
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        # Construct the molecule(s) that this udg really 'reflects'
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        # i.e. the udg has a central node and two cliques
        # that central node is the result of merging of several molecules
        # ideally, only one of those molecules is connected to the molecules of the cliques
        # (there could be more than one though; in that case the udg is 'ambiguous')
        # udg_molecules aims to reflect the molecule(s) underlying this udg
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        udg_molecules = set()

        # Get the current molecule idxs of central node
        molecule_idxs = mols_from_node(head[1])
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        # print("mol idxs", molecule_idxs)
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        # Examine molecule idx's of cliques to see which are close to the central node
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        # rationale: c1/c2 contain nearby molecule id's
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        for mol_idx in molecule_idxs:
            nexts = []
            for c in [c1,c2]:
                for c_node in c:
                    nei_mols = mols_from_node(c_node.split()[0])
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                    nei_mols = [x for x in nei_mols if x > mol_idx]  # fixme: also look at the <= molecules for more robustness
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                    # If there are molecule next
                    if len(nei_mols) > 0:
                        next_nei_mol = min(nei_mols)
                        nexts.append((next_nei_mol))

            nexts.sort(key=lambda x: x)
            quality = sum([1.0/x if mol_idx+x in nexts else 0 for x in range(1,6)]) / sum([1.0/x for x in range(1,6)])
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            if quality > 0.6:  # eyeballed but still arbitrary
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                udg_molecules.add(mol_idx)
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            # print("mol",mol_idx,molecule_idxs,"quality",quality,"nexts",nexts)
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        udg_molecules_dict[head[0]]=udg_molecules

    # Then: annotate edges as to whether they're real (their udg_molecule(s) are nearby) or fake
    for n1, n2 , data in d2_component.edges(data=True):
        # Parse the current node name
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        head, c1, c2 = parse_dg_name(d2_component,n1)
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        node_udg_molecules = udg_molecules_dict[head[0]]
        
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        n_head, n_c1, n_c2 = parse_dg_name(d2_component,n2)
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        neighbor_udg_molecules = udg_molecules_dict[n_head[0]]
       
        if nearby_udg_molecules(node_udg_molecules, neighbor_udg_molecules):
            color = 'green'
        else:
            color = 'red'
        data['color'] = color
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        # print("edge",node_udg_molecules,neighbor_udg_molecules,color)
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    # also, annotate nodes by their putative molecule found
    for n, data in d2_component.nodes(data=True):
        # Parse the current node name
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        head, c1, c2 = parse_dg_name(d2_component,n)
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        node_udg_molecules = udg_molecules_dict[head[0]]
        data['udg_molecule']= '_'.join(list(map(str,node_udg_molecules)))
        
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    # aggressive: delete nodes which have either no found udg_molecule, or two udg_molecules
    # turns out it's not a good strategy as the nodes with two udg_molecules are important to connect portions of graph
    # but what if we magically keep those where the two adjacent molecules are close together
    if True:
        d2_component = d2_component.copy()
        nodes_to_remove = []
        for n, data in d2_component.nodes(data=True):
            # Parse the current node name
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            head, c1, c2 = parse_dg_name(d2_component,n)
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            if "_" in data['udg_molecule'] or data['udg_molecule'] == '':
                if "_" in data['udg_molecule']:
                    m1, m2 = list(map(int,data['udg_molecule'].split("_")))
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                    if abs(m2-m1) < 30: continue  # don't remove that kind of nodes
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                nodes_to_remove += [n]
        d2_component.remove_nodes_from(nodes_to_remove)
        print("removed",len(nodes_to_remove),"bad nodes")

    # aggressive: delete red edges
    if True:
        d2_component = d2_component.copy()
        edges_to_remove = []
        for n1, n2, data in d2_component.edges(data=True):
            if data['color'] == 'red':
                edges_to_remove += [(n1,n2)]
        d2_component.remove_edges_from(edges_to_remove)
        print("removed",len(edges_to_remove),"bad edges")


    return d2_component
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def main():
    args = parse_args()
    graph = load_graph(args.filename)

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    if args.type == "path":
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        if args.barcode_graph is None:
            print("--barcode_graph is required for path analysis", file=sys.stderr)
            exit(0)

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        barcode_graph = load_graph(args.barcode_graph)
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        # if len(list(nx.connected_components(graph))) != 1:
        #     print([len(x) for x in list(nx.connected_components(graph))])
        #     exit("when running evaluate.py --type path, the graph should have a single connected component (it's supposed to be a path, after all)")
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        # compute LIS over the path
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        # longest_path = compute_longest_increasing_paths(graph)
        longest_path = compute_shortest_edit_path(graph)
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        print("--- Largest component analysis ---")
        print(f"Size of the longest path: {len(longest_path)}")
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        if not args.light_print:
            print(longest_path)
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        # get over/under counted molecules
        print("--- Under/over molecule counts ---")
        frequencies = parse_path_graph_frequencies(graph, barcode_graph)
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        print_path_summary(frequencies, light_print=args.light_print)
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        print(f"Size of the longest path: {len(longest_path)}")
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    elif args.type == "dgraphs":
        udg_per_node = parse_udg_qualities(graph)
        # print(udg_per_node)
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    elif args.type == "d2":
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        components = list(nx.connected_components(graph))
        components.sort(key=lambda x: -len(x))

        component = graph.subgraph(components[0])
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        longest_path = compute_longest_increasing_paths(component, max_gap=args.max_gap)
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        vars = compute_covered_variables(graph, longest_path)
        print_d2_summary(components, longest_path, coverage_vars=vars, light_print=args.light_print)
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    # added by Rayan
    # example:
    # python evaluate.py --type d2-2annotate ~/Dropbox/cnrs/projects/10x-barcodes/yoann_to_cedric_ilp/d2_graph.gexf
    elif args.type == "d2-2annotate":
        components = list(nx.connected_components(graph))
        components.sort(key=lambda x: -len(x))
        component = graph.subgraph(components[0])
 
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        component = verify_graph_edges(component)
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        extension = args.filename.split('.')[-1]
        base_filename = '.'.join(args.filename.split('.')[:-1])
        save_graph(component, base_filename+".verified."+extension)

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if __name__ == "__main__":
    main()