reactome_pathway.py

__author__ = "Hedra"
__email__ = "hedra@singularitynet.io"

# The following script imports Reactome pathways and their relationship from https://reactome.org

# Requires: 
	# https://reactome.org/download/current/ReactomePathwaysRelation.txt
	# https://reactome.org/download/current/ReactomePathways.txt

import pandas as pd
from urllib.request import urlopen
import os
import metadata
from datetime import date

# Helper functions

def eva(name, reid):
	if 'R-HSA' in reid:
		return ""+'(EvaluationLink \n \t(PredicateNode "has_name")\n \t(ListLink\n \t\t(ConceptNode "'+ reid.strip() + '")\n' + '\t\t(ConceptNode "'+ name.strip() + '")))\n'
	else:
		return ""

def inherit(parent, child):
	if 'R-HSA' in parent and 'R-HSA' in child:
		return ""+'(InheritanceLink \n \t(ConceptNode "'+ child.strip() + '")\n' + '\t(ConceptNode "'+ parent.strip() + '"))\n'
	else:
		return ""

# URL

pathway_rln = "https://reactome.org/download/current/ReactomePathwaysRelation.txt"
pathway = "https://reactome.org/download/current/ReactomePathways.txt"

if not os.path.isfile('ReactomePathwaysRelation.txt'):
	print("Downloading ReactomePathwaysRelation.txt")
	pathway_relation = pd.read_csv(urlopen(pathway_rln), low_memory=False, delimiter='\t', names=["parent", "child"])
	print("Done")
else:
	pathway_relation = pd.read_csv('ReactomePathwaysRelation.txt', low_memory=False, delimiter='\t', names=["parent", "child"])  

if not os.path.isfile('ReactomePathways.txt'):
	print("Downloading ReactomePathways.txt")
	pathway_list = pd.read_csv(urlopen(pathway), low_memory=False, delimiter='\t', names=["ID", "name", "Species"])
	print("Done")
else:
	pathway_list = pd.read_csv('ReactomePathways.txt', low_memory=False, delimiter='\t', names=["ID", "name", "Species"]) 

pathway_list = pathway_list[pathway_list['Species']=='Homo sapiens'] 
max_len = max(len(pathway_list), len(pathway_relation)) 

print("Started importing")

script = "https://github.com/MOZI-AI/knowledge-import/reactome_pathway.py"
pathways = pathway_relation['parent'].values + pathway_relation['child'].values
if not os.path.exists(os.path.join(os.getcwd(), 'dataset')):
    os.makedirs('dataset')
with open("dataset/reactome_{}.scm".format(str(date.today())), 'w') as f:
    for i in range(max_len):
        try:
            f.write(eva(pathway_list.iloc[i]['name'],pathway_list.iloc[i]['ID']))
            f.write(inherit(pathway_relation.iloc[i]['parent'], pathway_relation.iloc[i]['child']))
        except IndexError:
            f.write(inherit(pathway_relation.iloc[i]['parent'], pathway_relation.iloc[i]['child']))
num_pathways = {"Reactome Pathway": len(set(pathways))}
metadata.update_meta("Reactome Pathways relationship:latest", 
        pathway_rln+" "+pathway,script,pathways=num_pathways)

print("Done")