Commit 6976ef41 authored by Tiago Peixoto's avatar Tiago Peixoto

Add celegans_metabolic

parent 633ba5de
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
# details.
#
# You should have received a copy of the GNU Affero General Public License along
# with this program. If not, see <http://www.gnu.org/licenses/>.
from .. import *
title = "Metabolic network (C. elegans)"
description = """List of edges comprising the metabolic network of the nematode C. elegans.[^icon]
[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Biological', 'Metabolic', 'Unweighted']
url = 'https://deim.urv.cat/~alexandre.arenas/data/welcome.htm'
citation = [('J. Duch and A. Arenas, "Community identification using Extremal Optimization." Physical Review E 72, 027104 (2005).', 'http://arxiv.org/abs/cond-mat/0501368')]
icon_hash = '56a85c8e26855e083a2f78d6'
ustream_license = None
upstream_prefix = 'http://deim.urv.cat/~alexandre.arenas/data/xarxes'
files = [('celegans_metabolic.zip:celegans_metabolic.net', None, 'pajek')]
def fetch_upstream(force=False):
return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
force)
@cache_network()
@coerce_props()
@annotate()
def parse(alts=None):
global files
name = __name__.split(".")[-1]
for fnames, alt, fmt in files:
if alts is not None and alt not in alts:
continue
if isinstance(fnames, str):
fnames = [fnames]
with ExitStack() as stack:
fs = [stack.enter_context(open_upstream_file(name, fn, "rb")) for fn in fnames]
g = parse_graph(fs, fmt, directed=False)
yield alt, g
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