#!/usr/bin/env python3.3

from collections import defaultdict

import urllib.request

import csv

import gzip

from string import Template

import datetime

from bel_functions import bel_term

'''

Generates resource 'scaffolding' document for named complexes to be used with the BEL Compiler.

1. Identifies GOCC ID values that have the encoding 'C' (complex).

2. Downloads current GO Annotation files for human, mouse, and rat.

3. Validates values in GO annotation files as proteins ('GRP' encoding in .belns files).

4. Generates output file with complex hasComponent BEL statements.

'''

# name of output BEL file

output_file = 'named-complexes.bel'

# url for .belns document with complex, values are expected to be GO IDs

gocc_url = 'http://resources.openbel.org/belframework/testing/namespace/go-cellular-component-ids.belns'

# GO annotation file locations and associated namespaces

datasets = [

'RGD')]

def get_complexes(belns_url):

return complexes, complex_ns

def get_encoding_dict(belns_url):

return encoding_dict

# get complex ids from .belns file

complexes, complex_ns = get_complexes(gocc_url)

print('\nFound {0} complexes in {1}.'.format(len(complexes), gocc_url))

# info for bel script output file generation

annotations = {

'Species': 'http://resources.openbel.org/belframework/testing/annotation/species-taxonomy-id.belanno'}

namespaces = {

complex_ns: gocc_url}

today = datetime.date.today()

version = str(today.year) + str(today.month) + str(today.day)

separator = '#' * 50

# generate file header

with open(output_file, 'w') as bel:

bel.write(separator)

bel.write('\n# Document Properties Section\n')

bel.write('SET DOCUMENT Name = "GOCC Named Complex Scaffolding"\n')

bel.write('SET DOCUMENT Description = "Named Complex scaffolding for use with the BEL compiler. File is generated from GO gene association files for human, mouse and rat."\n')

bel.write('SET DOCUMENT Version = "{0}"\n'.format(version))

bel.write('SET DOCUMENT Copyright = "Copyright (c) {0}, OpenBEL Project. This work is licensed under a Creative Commons Attribution 3.0 Unported License."\n'.format(

str(today.year)))

bel.write('SET DOCUMENT Authors = "OpenBEL"\n')

bel.write('\n' + separator + '\n')

bel.write('# Definitions Section\n')

for ns, url in namespaces.items():

bel.write('DEFINE NAMESPACE {0} AS URL "{1}"\n'.format(ns, url))

for anno, url in annotations.items():

bel.write('DEFINE ANNOTATION {0} AS URL "{1}"\n'.format(anno, url))

bel.write(separator + '\n')

bel.write('# Statements Section\n\n')

# download and open human, mouse, and rat gene association files from GO (datasets)

# write BEL file for each species with genes annotated to each complex term

for (species, url, ns) in datasets:

# build dict to validate symbols as proteins

encoding_dict = get_encoding_dict(namespaces.get(ns))

date = ''

# TODO - save to output/datasets directory

print('Downloading {0} GO gene-associations data ...'.format(ns))

go = urllib.request.urlopen(url)

goa_file_name = url.split('/')[-1]

with open(goa_file_name, 'b+w') as f:

f.write(go.read())

# make dictionary genemap with list of proteins for each complex GO term

gomap = defaultdict(set)

with gzip.open(goa_file_name, mode='rt') as g:

reader = csv.reader(g, delimiter='\t')

for row in reader:

if row[0].startswith('!'):

if 'Submission Date:' in row:

date = row[0].split(':')[1].strip()

(month, day, year) = date.split('/')

date = Template(

'${year}-${month}-${day}').substitute(year=year, day=day, month=month)

else:

continue

# find records with CC GO terms, that do not have a qualifier

else:

goid = row[4].replace('GO:', '')

qualifier = row[3]

symbol = row[2]

if qualifier == '' and goid in complexes:

# convert complex into BEL term

term = bel_term(

row[4].replace(

'GO:',

''),

complex_ns,

'complex')

# convert symbol into BEL term, exclude non-protein symbols

if encoding_dict.get(symbol) == 'GRP':

gene = bel_term(symbol, ns, 'p')

gomap[term].add(gene)

# sort genes annotated to each complex in gomap

gomap = {k: sorted(list(v)) for k, v in gomap.items()}

print(

'\tGenerating {0} BEL hasComponents statements.\n'.format(

len(gomap)))

# create statements and associated annotations; append to output file

with open(output_file, 'a') as bel:

bel.write('SET Species = {0}\n'.format(species))

bel.write(

'SET Citation = {3}"Online Resource", "GO Annotation File - {0}", "{1}", "{2}", "", ""{4}\n\n'.format(

species, url, date, '{', '}'))

for k, v in gomap.items():

bel.write('{0} hasComponents list({1})\n'.format(k, ','.join(v)))

# bel.write(k + ' hasComponents list(' + ",".join(v) + ')')

# bel.write('\n')