"Parse downloaded KEGG pathways and save them in a simpler format"

from __future__ import print_function

import os.path

import sys

import os

import json

from Bio.KEGG.KGML import KGML_parser

import converter

cachedir = os.path.join(os.getenv("HOME"), "pathwaycache", "kegg_reboot")

kgmldir = os.path.join(cachedir, "kgml")

outdir = os.path.join(cachedir, "pathways")

if not os.path.exists(outdir):

os.makedirs(outdir)

INFO_SIGN = {

'activation' : "+",

'inhibition' : "-",

}

INFO_TYPE = {

}

INFO_IGNORED = set((

))

def uid_of(entry):

return entry.id

f_members = open(os.path.join(outdir, 'members.txt') , 'w')

for filename in os.listdir(kgmldir):

nodes = {}

pathway_nodes = set()

if not filename.endswith(".xml") or not filename.startswith("hsa"): continue

kgid = filename[:-4]

kgml_file = os.path.join(kgmldir, filename)

f = open(kgml_file)

print(filename)

parsed = KGML_parser.read(f)

f.close()

pathway_name = parsed.title

# Find and map components

components = set()

# Enter the parsed pathway info and extract components

for k,entry in parsed.entries.items():

if entry.type != "gene":

continue

rnames = entry.name.split(" ")

names = [ converter.handler.to_uniprot(converter.KEGG_IDX, u) for u in rnames ]

names = [ u for u in names if u ]

if not names:

# TODO: can we fix empty KEGG nodes?

print( "empty node??", rnames)

continue

components.update(names)

nodes['%s' % entry.id] = names

# Extract relations and save in normalized format

out = open(os.path.join(outdir, '%s.txt' % kgid), 'w')

relations = []

for rel in parsed.relations:

uid1 = uid_of(rel.entry1)

uid2 = uid_of(rel.entry2)

if not uid1 or not uid2:

continue

# Extract the type and sign

reltype = ''

sign = ''

for name,tag in rel.subtypes:

if name in INFO_SIGN:

sign = INFO_SIGN[name]

elif name in INFO_TYPE:

reltype = INFO_TYPE[name]

relations.append( (uid1,uid2, reltype, sign) )

if uid1 not in nodes or uid2 not in nodes:

continue

for n1 in nodes[uid1]:

for n2 in nodes[uid2]:

out.write('%s\t%s\t%s\t%s\n' % (n1, n2, reltype, sign))

pathway_nodes.add(n1)

pathway_nodes.add(n2)

f_members.write("%s\t%s\t%s\n" % (kgid, pathway_name, ','.join(pathway_nodes)))

out.close()

f_members.close()