Source code for

# -*- coding: utf-8 -*-

"""Convert a BEL graph to HiPathia inputs.

SIF File
- Text file with three columns separated by tabs.
- Each row represents an interaction in the pathway. First column is the source
  node, third column the target node, and the second is the type of relation
  between them.
- Only activation and inhibition interactions are allowed.
- The name of the nodes in this file will be stored as the IDs of the nodes.
- The nodes IDs should have the following structure: N (dash) pathway ID (dash)
  node ID.
- HiPathia distinguish between two types of nodes: simple and complex.

Simple nodes:

- Simple nodes may include many genes, but only one is needed to perform the
  function of the node. This could correspond to a protein family of enzymes
  that all have the same function - only one of them needs to be present for
  the action to take place. Simple nodes are defined within
- Node IDs from simple nodes do not include any space, i.e. N-hsa04370-11.

Complex nodes:

- Complex nodes include different simple nodes and represent protein complexes.
  Each simple node within the complex represents one protein in the complex.
  This node requires the presence of all their simple nodes to perform its
- Node IDs from complex nodes are the juxtaposition of the included simple node
  IDs, separated by spaces, i.e. N-hsa04370-10 26.

ATT File
Text file with twelve (12) columns separated by tabulars. Each row represents a node (either simple or complex).

The columns included are:

1. ``ID``: Node ID as explained above.
2. ``label``: Name to be shown in the picture of the pathway en HGNC. Generally, the gene name of the first
   included EntrezID gene is used as label. For complex nodes, we juxtapose the gene names of the first genes of
   each simple node included (see genesList column below).
3. ``X``: The X-coordinate of the position of the node in the pathway.
4. ``Y``: The Y-coordinate of the position of the node in the pathway.
5. ``color``: The default color of the node.
6. ``shape``: The shape of the node. "rectangle" should be used for genes and "circle" for metabolites.
7. ``type``: The type of the node, either "gene" for genes or "compound" for metabolites. For complex nodes, the
   type of each of their included simple nodes is juxtaposed separated by commas, i.e. gene,gene.
8. ``label.cex``: Amount by which plotting label should be scaled relative to the default.
9. ``label.color``: Default color of the node.
10. ``width``: Default width of the node.
11. ``height``: Default height of the node.
12. ``genesList``: List of genes included in each node, with EntrezID:

  - Simple nodes: EntrezIDs of the genes included, separated by commas (",") and no spaces, i.e. 56848,8877 for
    node N-hsa04370-11.
  - Complex nodes: GenesList of the simple nodes included, separated by a slash ("/") and no spaces, and in the
    same order as in the node ID. For example, node N-hsa04370-10 26 includes two simple nodes: 10 and 26. Its
    genesList column is 5335,5336,/,9047, meaning that the genes included in node 10 are 5335 and 5336, and the
    gene included in node 26 is 9047.


import logging
import os
from collections import defaultdict
from itertools import groupby
from operator import itemgetter
from typing import List, Optional, Set, Tuple, Union

import networkx as nx
import pandas as pd

from ..dsl import ComplexAbundance, Protein, hgnc
from ..struct import BELGraph

__all__ = [

logger = logging.getLogger(__name__)

ATT_COLS = ['ID', 'label', 'genesList']

[docs]def from_hipathia_paths(name: str, att_path: str, sif_path: str) -> BELGraph: """Get a BEL graph from HiPathia files.""" att_df = pd.read_csv(att_path, sep='\t') sif_df = pd.read_csv(sif_path, sep='\t', header=None, names=['source', 'relation', 'target']) return from_hipathia_dfs(name=name, att_df=att_df, sif_df=sif_df)
def group_delimited_list(entries: List[str], sep: str = '/') -> List[List[str]]: """Group delimited things in a list.""" return [ list(b) for a, b in groupby(entries, lambda z: z == sep) if not a ] def _p(identifier: str): return Protein( namespace='ncbigene', identifier=identifier, # name=name, ) def _f(identifier: str): return Protein( namespace='', identifier=identifier, # name=name, )
[docs]def from_hipathia_dfs(name: str, att_df: pd.DataFrame, sif_df: pd.DataFrame) -> BELGraph: """Get a BEL graph from HiPathia dataframes.""" def _clean_name(s): prefix = 'N-{name}-'.format(name=name) if prefix not in s: raise ValueError('wrong name for pathway') return tuple(sorted(s[len(prefix):].split(' '))) att_df['ID'] = att_df['ID'].map(_clean_name) att_df['label'] = att_df['label'].str.split(' ') att_df['genesList'] = att_df['genesList'].str.split(',').map(group_delimited_list) simple_node_to_dsl = {} family_node_to_dsl = {} complex_node_to_dsl = {} graph = BELGraph(name=name) for components, component_label_lists, component_gene_lists in att_df[['ID', 'label', 'genesList']].values: if not components: print(att_df[['ID', 'label', 'genesList']]) raise ValueError('missing components in row') if len(components) == 1: # This is a simple node, representing a protein or protein family component, label, entrez_ids = components[0], component_label_lists[0], component_gene_lists[0] if len(entrez_ids) == 1: # just a protein simple_node_to_dsl[component] = _p(identifier=entrez_ids[0]) else: # a protein family family_dsl = _f(identifier=label) for entrez_id in entrez_ids: child_dsl = _p(entrez_id) graph.add_is_a(child_dsl, family_dsl) family_node_to_dsl[component] = family_dsl else: # This is a complex node, representing a protein complex of simple nodes component_dsls = [] components = tuple(sorted(components)) for component, label, entrez_ids in zip(components, component_label_lists, component_gene_lists): if len(entrez_ids) == 1: simple_dsl = _p(identifier=entrez_ids[0]) simple_node_to_dsl[component] = simple_dsl component_dsls.append(simple_dsl) else: family_dsl = _f(identifier=label) for entrez_id in entrez_ids: child_dsl = _p(identifier=entrez_id) graph.add_is_a(child_dsl, family_dsl) family_node_to_dsl[component] = family_dsl component_dsls.append(family_dsl) component_dsl = ComplexAbundance(component_dsls) graph.add_node_from_data(component_dsl) complex_node_to_dsl[components] = component_dsl # Remap all of the dictionaries x = {} x.update(complex_node_to_dsl) for k, v in simple_node_to_dsl.items(): x[(k,)] = v for k, v in family_node_to_dsl.items(): x[(k,)] = v sif_df['source'] = sif_df['source'].map(_clean_name).map(x.get) sif_df['target'] = sif_df['target'].map(_clean_name).map(x.get) for source, relation, target in sif_df.values: if relation == 'activation': graph.add_increases(source, target, citation=(CITATION_TYPE_OTHER, 'HiPathia'), evidence='') elif relation == 'inhibition': graph.add_decreases(source, target, citation=(CITATION_TYPE_OTHER, 'HiPathia'), evidence='') else: raise ValueError('unknown relation: {relation}'.format(relation=relation)) return graph
[docs]def to_hipathia( graph: BELGraph, directory: str, draw: bool = True, ) -> None: """Export HiPathia artifacts for the graph.""" att_df, sif_df = to_hipathia_dfs(graph, draw_directory=directory if draw else None) if att_df is None and sif_df is None: logger.warning('can not convert graph %s', return att_df.to_csv(os.path.join(directory, '{}.att'.format(, sep='\t', index=False) sif_df.to_csv(os.path.join(directory, '{}.sif'.format(, sep='\t', index=False)
def _is_node_family(graph: BELGraph, node: Protein) -> Optional[Set[Protein]]: """Get the children of the protein node, if some exist.""" children = set() for child, _, data in graph.in_edges(node, data=True): if data[RELATION] == IS_A: children.add(child) if children and not all(isinstance(child, Protein) for child in children): logger.warning('not all children of {} are proteins: {}'.format(node, children)) return return children
[docs]def to_hipathia_dfs( graph: BELGraph, draw_directory: Optional[str] = None, ) -> Union[Tuple[None, None], Tuple[pd.DataFrame, pd.DataFrame]]: """Get the ATT and SIF dataframes. :param graph: A BEL graph :param draw_directory: The directory in which a drawing should be output 1. Identify nodes: 1. Identify all proteins 2. Identify all protein families 3. Identify all complexes with just a protein or a protein family in them 2. Identify interactions between any of those things that are causal 3. Profit! """ proteins = set() families = defaultdict(set) complexes = set() for node in sorted(graph, key=str): if isinstance(node, Protein): children = _is_node_family(graph, node) if children: families[node] = children else: proteins.add(node) elif isinstance(node, ComplexAbundance) and all(isinstance(m, Protein) for m in node.members): complexes.add(node) families = { node: sorted(values, key=str) for node, values in sorted(families.items(), key=itemgetter(0)) } nodes = sorted(proteins.union(families).union(complexes), key=str) new_nodes = set() edges = [] for u, v, _, d in sorted(graph.out_edges(nodes, keys=True, data=True), key=lambda t: (str(t[0]), str(t[1]), t[2])): relation = d[RELATION] if relation not in CAUSAL_POLAR_RELATIONS: continue new_nodes.add(u) new_nodes.add(v) edges.append((u, 'activation' if relation in CAUSAL_INCREASE_RELATIONS else 'inhibition', v)) att = {} dsl_to_k = {} i = 0 for node in sorted(new_nodes, key=str): if node in families: i += 1 k = (i,) children = families[node] child_identifiers = [child.identifier for child in children] if not all(child_identifiers): logger.warning('not all children were grounded: %s', child_identifiers) continue labels, genes_lists = [], [child_identifiers] elif isinstance(node, Protein): if not node.identifier or not logger.warning('node was not grounded: %s', node) continue i += 1 k = (i,) labels, genes_lists = [], [[node.identifier]] elif isinstance(node, ComplexAbundance): k, labels, genes_lists = [], [], [] for member in node.members: i += 1 k.append(i) labels.append( if member in families: children = families[member] child_identifiers = [child.identifier for child in children] if not all(child_identifiers): logger.warning('not all children were grounded: %s', child_identifiers) continue genes_lists.append(child_identifiers) else: if not member.identifier: logger.warning('member was not grounded: %s', member) continue genes_lists.append([member.identifier]) k = tuple(k) else: logger.debug('skipping node {}'.format(node)) continue k = 'N-{}-{}'.format(, ' '.join(map(str, k))) att[k] = labels, genes_lists dsl_to_k[node] = k edges = [ (dsl_to_k[source], relation, dsl_to_k[target]) for source, relation, target in edges if source in dsl_to_k and target in dsl_to_k ] sif_df = pd.DataFrame(edges) # DONE composite_graph = nx.Graph([(k_source, k_target) for k_source, _, k_target in edges]) try: from networkx.drawing.nx_agraph import pygraphviz_layout pos = pygraphviz_layout(composite_graph, prog="neato", args='-Gstart=5') except ImportError: logger.warning('could not import pygraphviz. Falling back to force directed') pos = nx.fruchterman_reingold_layout(composite_graph, seed=5) if not pos: return None, None nx_labels = {} # from k to label min_x = min(x for x, y in pos.values()) min_y = min(y for x, y in pos.values()) att_rows = [] for k, (labels, genes_lists) in sorted(att.items()): if k not in pos: logger.warning('node not in graph: %s', k) continue nx_labels[k] = label = ' '.join(labels) types = ','.join(['gene'] * len(labels)) gene_list = ',/,'.join( ','.join(gene_list) for gene_list in genes_lists ) x, y = pos[k] att_rows.append(( k, # 1. ID label, # 2. label int(100 * (x - min_x)), # 3. X int(100 * (y - min_y)), # 4. Y 'white', # 5. color 'rectangle', # 6. shape types, # 7. 0.5, # 8. label.cex 'black', # 9. label.color 46, # 10. width 17, # 11. height gene_list, # 12. gene list )) att_df = pd.DataFrame(att_rows, columns=[ 'ID', 'label', 'X', 'Y', 'color', 'shape', 'type', 'label.cex', 'label.color', 'width', 'height', 'genesList' ]) if draw_directory is not None: try: import matplotlib.pyplot as plt except ImportError: logger.warning('could not draw graph because matplotlib is not installed') else: plt.figure(figsize=(20, 20)) nx.draw_networkx(composite_graph, pos, labels=nx_labels) plt.axis('off') plt.savefig(os.path.join(draw_directory, '{}.png'.format( return att_df, sif_df
def make_hsa047370() -> BELGraph: """Make an example BEL graph corresponding to the example data from Marina.""" graph = BELGraph(name='hsa04370') node_1 = hgnc(name='CDC42') node_9 = hgnc(name='KDR') node_11 = hgnc(name='SPHK2') node_17 = hgnc(name='MAPKAPK3') node_18 = hgnc(name='PPP3CA') node_19 = hgnc(name='AKT3') node_20 = hgnc(name='PIK3R5') node_21 = hgnc(name='NFATC2') node_22 = hgnc(name='PRKCA') node_24 = hgnc(name='MAPK14') node_27 = hgnc(name='SRC') node_29 = hgnc(name='VEGFA') node_32 = hgnc(name='MAPK1') node_33 = hgnc(name='MAP2K1') node_34 = hgnc(name='RAF1') node_35 = hgnc(name='HRAS') node_10 = ComplexAbundance([hgnc(name='PLCG1'), hgnc(name='SH2D2A')]) node_28 = hgnc(name='SHC2') node_23 = hgnc(name='PTK2') node_25 = hgnc(name='PXN') node_16 = hgnc(name='HSPB1') node_36 = hgnc(name='NOS3') node_37 = hgnc(name='CASP9') node_38 = hgnc(name='BAD') node_39 = hgnc(name='RAC1') node_14 = hgnc(name='PTGS2') node_15 = hgnc(name='PLA2G4B') def _add_increases(a, b): graph.add_directly_increases(a, b, citation='', evidence='') def _add_decreases(a, b): graph.add_directly_decreases(a, b, citation='', evidence='') _add_increases(node_1, node_24) _add_increases(node_9, node_28) _add_increases(node_9, node_23) _add_increases(node_9, node_25) _add_increases(node_9, node_20) _add_increases(node_9, node_27) _add_increases(node_9, node_10) _add_increases(node_11, node_35) _add_increases(node_17, node_16) _add_increases(node_18, node_21) _add_increases(node_19, node_36) _add_decreases(node_19, node_37) _add_decreases(node_19, node_38) _add_increases(node_20, node_39) _add_increases(node_20, node_19) _add_increases(node_21, node_14) _add_increases(node_22, node_34) _add_increases(node_22, node_11) _add_increases(node_24, node_17) _add_increases(node_27, node_20) _add_increases(node_29, node_9) _add_increases(node_32, node_15) _add_increases(node_33, node_32) _add_increases(node_34, node_33) _add_increases(node_35, node_34) _add_increases(node_10, node_18) _add_increases(node_10, node_22) _add_increases(node_10, node_15) _add_increases(node_10, node_36) return graph