History of yeast_spliceosome
The changes to the source code of this entry in the repository, newest first, each with the differences it made to the entry's files. They are also listed on GitLab.
[entries] New entry: yeast_spliceosome 86eaa32
diff --git a/entries/yeast_spliceosome/__init__.py b/entries/yeast_spliceosome/__init__.py
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+++ b/entries/yeast_spliceosome/__init__.py
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+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2020-2026 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 = "Yeast spliceosome protein interactions (2017)"
+description = """Weighted network of interactions among the proteins of the spliceosome of the yeast *Saccharomyces cerevisiae*, as compiled by M. Cantor and collaborators in a study of nestedness across levels of biological organization. Nodes are 103 spliceosome proteins, and an undirected edge connects two proteins with evidence of a physical association between them in the STRING database (2011 version); edges are weighted by STRING's score, the combined reliability of the evidence for the interaction (from 0, no evidence, to 1, strong support), which estimates the probability that the interaction is correct. The network is dense (connectance 0.78). The proteins are not identified in the source data.
+
+The edges have the property `weight`, the STRING score of the interaction.[^icon]
+
+[^icon]: Description obtained in part from the [ICON](https://icon.colorado.edu) project."""
+tags = ['Biological', 'Protein interactions', 'Weighted']
+url = 'https://bitbucket.org/maucantor/unodf_analyses'
+citation = [('M. Cantor, M. M. Pires, F. M. D. Marquitti, R. L. G. Raimundo, E. Sebastián-González, P. P. Coltri, S. I. Perez, D. R. Barneche, D. Y. C. Brandt, K. Nunes, F. G. Daura-Jorge, S. R. Floeter, P. R. Guimarães Jr., "Nestedness across biological scales." PLoS ONE 12(2), e0171691 (2017)', 'https://doi.org/10.1371/journal.pone.0171691'),
+ ('D. Szklarczyk, A. Franceschini, M. Kuhn, M. Simonovic, A. Roth, P. Minguez, T. Doerks, M. Stark, J. Muller, P. Bork, L. J. Jensen, C. von Mering, "The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored." Nucleic Acids Research 39, D561-D568 (2011)', 'https://doi.org/10.1093/nar/gkq973')]
+icon_hash = '5c3e6ed55cc47b871aed53cb'
+upstream_license = None
+upstream_prefix = 'https://bitbucket.org/maucantor/unodf_analyses/raw/cef0977496fcb93ec72d20d8c37f0dd46b9f18be/data'
+files = [('mol_yeast_spliceosome.txt', None, None)]
+
+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 fname, alt, fmt in files:
+ if alts is not None and alt not in alts:
+ continue
+ with open_upstream_file(name, fname, "r") as f:
+ A = numpy.loadtxt(f)
+ g = adjacency_graph(A, directed=False)
+ yield alt, g