History of interactome_yeast
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] Add the date when each entry was added, and remove icon_hash beff7c9
The dates are those of the commits that first added the entries' files (2020-08-11 for the entries of the initial commit); renamed entries keep the date of their first name. Changed: none
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index d9807b8..e280ca1 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -34,7 +34,7 @@ url = ['https://web.archive.org/web/20060812145625/http://www.nd.edu/~networks/r
'https://web.archive.org/web/20210115130726/http://moreno.ss.uci.edu/data.html#pro-pro']
citation = [('H. Jeong, S. P. Mason, A.-L. Barabási, Z. N. Oltvai, "Lethality and centrality in protein networks." Nature 411, 41-42 (2001)', 'https://doi.org/10.1038/35075138'),
('S. Coulomb et al. "Gene essentiality and the topology of protein interaction networks." Proc. Roy. Soc. London B: Biological Sciences 272(1573), 1721-1725 (2005).', 'https://doi.org/10.1098/rspb.2005.3128')]
-icon_hash = ['581761258cf714f319c3e77c', '56a85c8e26855e083a2f78e3']
+date_added = '2020-08-11'
upstream_license = None
upstream_prefix = 'https://web.archive.org/web/20061110233005id_/http://www.nd.edu:80/%7Enetworks/resources/protein'
files = [(('bo.dat.gz', 'pronam.dat'), None, None)]
[entries] Prefix the properties in the descriptions with (Node), (Edge) or (Graph) bc3dbbd
The lists of properties at the end of the descriptions marked edge properties with "Edge" but left node properties unmarked, or grouped them in "Nodes: `a`, ...; `b`, ..." items, so the kind of a property was often unclear. Every item now starts with (Node), (Edge) or (Graph), followed by the property names, a colon and the explanation, one item per property or group of properties; qualifications (kinds of nodes, networks) follow the names in parentheses. Properties that were only named got a short explanation, and a few items that named the wrong kind of property were corrected.
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index f3d3d72..d9807b8 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -25,7 +25,10 @@ An undirected edge (i, j) indicates an interaction between proteins i and j. The
The network has the following properties:
-- Nodes: `protein_id`, the number of the protein in the source files; `orf`, the systematic (ORF) name of the gene (missing for 35 proteins); `name`, the standard gene name; `lethality`, whether the deletion of the gene is lethal ("Lethal", "Non-Lethal" or "Unknown")."""
+- (Node) `protein_id`: the number of the protein in the source files.
+- (Node) `orf`: the systematic (ORF) name of the gene (missing for 35 proteins).
+- (Node) `name`: the standard gene name.
+- (Node) `lethality`: whether the deletion of the gene is lethal ("Lethal", "Non-Lethal" or "Unknown")."""
tags = ['Biological', 'Protein interactions', 'Unweighted', 'Metadata']
url = ['https://web.archive.org/web/20060812145625/http://www.nd.edu/~networks/resources.htm',
'https://web.archive.org/web/20210115130726/http://moreno.ss.uci.edu/data.html#pro-pro']
[entries] Remove unneeded code from the entries 2c69f19
Unneeded "global files" statements, unused imports and variables, f-strings without placeholders, duplicate keys in foodweb_little_rock (keeping the order and the values used), and the second definition of get_lines() in twitter_higgs. Nothing changes in the networks or descriptions. Changed: none
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index d5f9af8..f3d3d72 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -52,7 +52,6 @@ def fetch_upstream(force=False):
"lethality": "string"})
@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:
[entries] Merge duplicate entries and add cross-references between related ones 9bc6033
- Removed duplicates, merged into the entries holding the same data: dblp_coauthor_snap (soc_net_comms), cattle and bison (dom; bison's breeding data move there, as do the wolves' age and sex), football_tsevans (football, with both conference assignments), eu_procurements_alt (eu_procurements), foursquare_friendships (foursquare_global). - software_dependencies: colt and scolt are one network; ambassador: the duplicate 2001 network is dropped and the three same-edge networks combined; dom: the dataset count corrected (436). - macaque_neural: Young's 71-area network added (young71; the 47-area one is now cocomac47), both from archived copies. - collins_yeast, celegans_interactomes: from archived copies of the dead CCSB site (byte-identical files). - Cross-references between entries holding versions of the same data (food webs, Wikipedia, Slashdot, physicians, SNAP/Mislove, CCSB). - ICON ids of duplicate records added; macaque_neural's corrected. - prosper, dbpedia_all: string properties given in edge-index order (needs graph-tool with the fixed vals ordering).
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index 7b76234..d5f9af8 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -31,7 +31,7 @@ url = ['https://web.archive.org/web/20060812145625/http://www.nd.edu/~networks/r
'https://web.archive.org/web/20210115130726/http://moreno.ss.uci.edu/data.html#pro-pro']
citation = [('H. Jeong, S. P. Mason, A.-L. Barabási, Z. N. Oltvai, "Lethality and centrality in protein networks." Nature 411, 41-42 (2001)', 'https://doi.org/10.1038/35075138'),
('S. Coulomb et al. "Gene essentiality and the topology of protein interaction networks." Proc. Roy. Soc. London B: Biological Sciences 272(1573), 1721-1725 (2005).', 'https://doi.org/10.1098/rspb.2005.3128')]
-icon_hash = '581761258cf714f319c3e77c'
+icon_hash = ['581761258cf714f319c3e77c', '56a85c8e26855e083a2f78e3']
upstream_license = None
upstream_prefix = 'https://web.archive.org/web/20061110233005id_/http://www.nd.edu:80/%7Enetworks/resources/protein'
files = [(('bo.dat.gz', 'pronam.dat'), None, None)]
[entries] Move more KONECT-derived entries to their original sources bf9dc0e
The entries now download the data from where KONECT obtained them (live, or via the Wayback Machine), using the same release as KONECT where it is still available, and gain the metadata KONECT dropped; descriptions and citations are rewritten from the original sources: - Linton Freeman's UCINET data page: bible_nouns, bison, cattle, hens, highschool, kangaroo, macaques, moreno_sheep, physician_trust (the three relations and the physicians' attributes), rhesus_monkey, train_terrorists, windsurfers (now the networks `interaction` and `closeness`), college_freshmen, crime, interactome_yeast (from the primary source), moreno_taro (undirected), residence_hall, zebras - other pages, archived: contiguous_usa, advogato, google, github, digg_reply, twitter, bookcrossing, dbtropes_feature (without KONECT's spurious "ItemName" tropes) - movielens_100k (in fact the MovieLens 10M tag assignments) - dblp release 2017-05-02: dblp_author_paper, dblp_cite, dblp_coauthor - DBpedia 3.9: dbpedia_country, dbpedia_genre, dbpedia_location, dbpedia_occupation, dbpedia_producer, dbpedia_recordlabel, dbpedia_starring, dbpedia_team, dbpedia_writer, dbpedia_all, dbpedia_link - Discogs releases dump of October 2015: discogs_affiliation, discogs_genre and discogs_label (now with genre and style networks)
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index 76183c3..7b76234 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -18,22 +18,38 @@
from .. import *
-title = "Coulomb yeast interactome (2005)"
-description = """A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
-tags = ['Biological', 'Protein interactions', 'Unweighted']
-url = 'http://konect.cc/networks/moreno_propro'
-citation = [('S. Coulomb et al. "Gene essentiality and the topology of protein interaction networks." Proc. Roy. Soc. London B: Biological Sciences 272(1573), 1721-1725 (2005).', 'https://doi.org/10.1098/rspb.2005.3128')]
+title = "Jeong yeast interactome (2001)"
+description = """Protein-protein interactions in yeast (Saccharomyces cerevisiae), studied by H. Jeong, S. P. Mason, A.-L. Barabási and Z. N. Oltvai (2001), who found that highly connected proteins are more likely to be essential (lethal if removed) than proteins of lower degree; later studies (e.g. S. Coulomb et al., 2005) argued that this result could be an artifact of the incompleteness of the data. The interactions were distributed by the Barabási lab at the University of Notre Dame (no longer online), from which this version was obtained via the Internet Archive. The protein names and lethalities were distributed, together with the same interactions, by L. C. Freeman on his network data page at the University of California, Irvine (no longer online), also obtained via the Internet Archive.
+
+An undirected edge (i, j) indicates an interaction between proteins i and j. The data contain self-loops. The protein list of L. C. Freeman contains 244 additional proteins without any interaction, which are not included.
+
+The network has the following properties:
+
+- Nodes: `protein_id`, the number of the protein in the source files; `orf`, the systematic (ORF) name of the gene (missing for 35 proteins); `name`, the standard gene name; `lethality`, whether the deletion of the gene is lethal ("Lethal", "Non-Lethal" or "Unknown")."""
+tags = ['Biological', 'Protein interactions', 'Unweighted', 'Metadata']
+url = ['https://web.archive.org/web/20060812145625/http://www.nd.edu/~networks/resources.htm',
+ 'https://web.archive.org/web/20210115130726/http://moreno.ss.uci.edu/data.html#pro-pro']
+citation = [('H. Jeong, S. P. Mason, A.-L. Barabási, Z. N. Oltvai, "Lethality and centrality in protein networks." Nature 411, 41-42 (2001)', 'https://doi.org/10.1038/35075138'),
+ ('S. Coulomb et al. "Gene essentiality and the topology of protein interaction networks." Proc. Roy. Soc. London B: Biological Sciences 272(1573), 1721-1725 (2005).', 'https://doi.org/10.1098/rspb.2005.3128')]
icon_hash = '581761258cf714f319c3e77c'
-upstream_prefix = 'http://konect.cc/files'
-files = [('download.tsv.moreno_propro.tar.bz2', None, 'konect')]
+upstream_license = None
+upstream_prefix = 'https://web.archive.org/web/20061110233005id_/http://www.nd.edu:80/%7Enetworks/resources/protein'
+files = [(('bo.dat.gz', 'pronam.dat'), None, None)]
+# the interactions (Barabási lab) and the protein names (L. C. Freeman) come
+# from different sites
+archived_urls = {
+ 'bo.dat.gz': upstream_prefix + '/bo.dat.gz',
+ 'pronam.dat': 'https://web.archive.org/web/20210115130726id_/http://moreno.ss.uci.edu/pronam.dat'}
def fetch_upstream(force=False):
- return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
- force)
+ # The Wayback Machine refuses connections or fails when rate-limited, so
+ # retry with increasing pauses (files already fetched are skipped)
+ return fetch_archived_files(__name__.split(".")[-1], archived_urls, force,
+ tries=6)
@cache_network()
-@coerce_props()
+@coerce_props(vforce={"orf": "string", "name": "string",
+ "lethality": "string"})
@annotate()
def parse(alts=None):
global files
@@ -44,6 +60,27 @@ def parse(alts=None):
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=True)
+ fs = [stack.enter_context(open_upstream_file(name, fn, "rb"))
+ for fn in fnames]
+ # each interaction is listed in both directions, and each
+ # self-loop once
+ E = numpy.loadtxt(fs[0], dtype="int") # decompressed on opening
+ lines = fs[1].read().decode("latin-1").replace("\r", "\n").split("\n")
+ prot = {}
+ for l in lines[lines.index("DATA:") + 1:]:
+ if not l.strip():
+ continue
+ # "number,orf,name,lethality"; when the ORF is missing, the line
+ # has the form "number,,,name,lethality"
+ x = l.split(",")
+ assert len(x) in [4, 5] and (len(x) == 4 or x[1:3] == ["", ""])
+ prot[int(x[0])] = (x[1] if len(x) == 4 else "", x[-2], x[-1])
+ E = E[E[:, 0] <= E[:, 1]]
+ g = Graph(directed=False)
+ vmap = g.add_edge_list(E, hashed=True)
+ assert all(int(i) in prot for i in vmap)
+ g.vp.protein_id = vmap
+ g.vp.orf = g.new_vp("string", vals=[prot[int(i)][0] for i in vmap])
+ g.vp.name = g.new_vp("string", vals=[prot[int(i)][1] for i in vmap])
+ g.vp.lethality = g.new_vp("string", vals=[prot[int(i)][2] for i in vmap])
yield alt, g
Update copyright information 73a4f0d
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index 6e761c9..76183c3 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2020-2024 Tiago de Paula Peixoto <tiago@skewed.de>
+# 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
Update copyright information 3d288ea
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index 2810d92..6e761c9 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2020-2023 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2024 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
Update copyright information 8d005ae
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index e9503f3..2810d92 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2021 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2023 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
Update copyright info db2efcc
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index 7644455..e9503f3 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -1,7 +1,7 @@
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
-# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2021 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
Un-orphan KONECT datasets 894eba5
KONECT has been brought back from the dead for the time being.
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index 2a90071..7644455 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -26,7 +26,6 @@ url = 'http://konect.cc/networks/moreno_propro'
citation = [('S. Coulomb et al. "Gene essentiality and the topology of protein interaction networks." Proc. Roy. Soc. London B: Biological Sciences 272(1573), 1721-1725 (2005).', 'https://doi.org/10.1098/rspb.2005.3128')]
icon_hash = '581761258cf714f319c3e77c'
upstream_prefix = 'http://konect.cc/files'
-orphan = True
files = [('download.tsv.moreno_propro.tar.bz2', None, 'konect')]
def fetch_upstream(force=False):
Update citations to use DOIs e878874
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index f7e41a2..2a90071 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -23,7 +23,7 @@ description = """A network of protein-protein binding interactions among yeast p
[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Biological', 'Protein interactions', 'Unweighted']
url = 'http://konect.cc/networks/moreno_propro'
-citation = [('S. Coulomb et al. "Gene essentiality and the topology of protein interaction networks." Proc. Roy. Soc. London B: Biological Sciences 272(1573), 1721-1725 (2005).', 'http://rspb.royalsocietypublishing.org/content/272/1573/1721.short')]
+citation = [('S. Coulomb et al. "Gene essentiality and the topology of protein interaction networks." Proc. Roy. Soc. London B: Biological Sciences 272(1573), 1721-1725 (2005).', 'https://doi.org/10.1098/rspb.2005.3128')]
icon_hash = '581761258cf714f319c3e77c'
upstream_prefix = 'http://konect.cc/files'
orphan = True
Add support for 'orphan' datasets and tag konect entries e330b80
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index 60a4f53..f7e41a2 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -26,6 +26,7 @@ url = 'http://konect.cc/networks/moreno_propro'
citation = [('S. Coulomb et al. "Gene essentiality and the topology of protein interaction networks." Proc. Roy. Soc. London B: Biological Sciences 272(1573), 1721-1725 (2005).', 'http://rspb.royalsocietypublishing.org/content/272/1573/1721.short')]
icon_hash = '581761258cf714f319c3e77c'
upstream_prefix = 'http://konect.cc/files'
+orphan = True
files = [('download.tsv.moreno_propro.tar.bz2', None, 'konect')]
def fetch_upstream(force=False):
Change license from GPLv3 to AGPLv3 d754be5
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index 9ecf0a7..60a4f53 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -3,18 +3,18 @@
#
# 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 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 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 General Public License for more details.
+# 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 General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# 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 *
Add explicit attribution to descriptions obtained from ICON 1645314
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
index f5d31df..9ecf0a7 100644
--- a/entries/interactome_yeast/__init__.py
+++ b/entries/interactome_yeast/__init__.py
@@ -19,7 +19,8 @@
from .. import *
title = "Coulomb yeast interactome (2005)"
-description = "A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins."
+description = """A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Biological', 'Protein interactions', 'Unweighted']
url = 'http://konect.cc/networks/moreno_propro'
citation = [('S. Coulomb et al. "Gene essentiality and the topology of protein interaction networks." Proc. Roy. Soc. London B: Biological Sciences 272(1573), 1721-1725 (2005).', 'http://rspb.royalsocietypublishing.org/content/272/1573/1721.short')]
Initial commit cc85872
diff --git a/entries/interactome_yeast/__init__.py b/entries/interactome_yeast/__init__.py
new file mode 100644
index 0000000..f5d31df
--- /dev/null
+++ b/entries/interactome_yeast/__init__.py
@@ -0,0 +1,48 @@
+#! /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 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 General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+from .. import *
+
+title = "Coulomb yeast interactome (2005)"
+description = "A network of protein-protein binding interactions among yeast proteins. Nodes represent proteins found in yeast (Saccharomyces cerevisiae) and an edge represents a binding interaction between two proteins."
+tags = ['Biological', 'Protein interactions', 'Unweighted']
+url = 'http://konect.cc/networks/moreno_propro'
+citation = [('S. Coulomb et al. "Gene essentiality and the topology of protein interaction networks." Proc. Roy. Soc. London B: Biological Sciences 272(1573), 1721-1725 (2005).', 'http://rspb.royalsocietypublishing.org/content/272/1573/1721.short')]
+icon_hash = '581761258cf714f319c3e77c'
+upstream_prefix = 'http://konect.cc/files'
+files = [('download.tsv.moreno_propro.tar.bz2', None, 'konect')]
+
+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=True)
+ yield alt, g