[med-svn] [Git][med-team/ragout][master] 2 commits: Adapt to python-networkx >= 2 (Thanks a lot to Tatiana Malygina...
Andreas Tille
gitlab at salsa.debian.org
Tue Mar 26 10:53:20 GMT 2019
Andreas Tille pushed to branch master at Debian Med / ragout
Commits:
76c27fff by Andreas Tille at 2019-03-26T10:51:09Z
Adapt to python-networkx >= 2 (Thanks a lot to Tatiana Malygina <merlettaia at gmail.com> for the patches)
- - - - -
12f1dde8 by Andreas Tille at 2019-03-26T10:52:35Z
Versioned (Build-)Depends python-networkx (since now this fails for version 1.x)
- - - - -
5 changed files:
- debian/control
- + debian/patches/d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0.patch
- + debian/patches/e3a06ef1256cf132903bbf19c9d4e11ea846e6df.patch
- + debian/patches/f4d4e2223a337abdbc5873fd6560e1494e55342d.patch
- debian/patches/series
Changes:
=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Priority: optional
Build-Depends: debhelper (>= 12~),
dh-python,
python-dev,
- python-networkx
+ python-networkx (>= 2.2)
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/ragout
Vcs-Git: https://salsa.debian.org/med-team/ragout.git
@@ -18,7 +18,7 @@ Depends: ${shlibs:Depends},
${python:Depends},
${misc:Depends},
sibelia,
- python-networkx
+ python-networkx (>= 2.2)
Description: Reference-Assisted Genome Ordering UTility
Ragout (Reference-Assisted Genome Ordering UTility) is a tool for
chromosome-level scaffolding using multiple references. Given initial
=====================================
debian/patches/d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0.patch
=====================================
@@ -0,0 +1,112 @@
+From d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0 Mon Sep 17 00:00:00 2001
+From: Tatiana Malygina <merlettaia at gmail.com>
+Date: Mon, 25 Mar 2019 16:09:21 +0300
+Origin: https://github.com/fenderglass/Ragout/pull/41
+Subject: [PATCH] replace edges_iter iterator with edges iterator in networkx
+ graphs
+
+---
+ ragout/breakpoint_graph/breakpoint_graph.py | 2 +-
+ ragout/breakpoint_graph/chimera_detector.py | 2 +-
+ ragout/breakpoint_graph/inferer.py | 4 ++--
+ ragout/scaffolder/merge_iters.py | 4 ++--
+ scripts/debug-report.py | 6 +++---
+ 5 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/ragout/breakpoint_graph/breakpoint_graph.py b/ragout/breakpoint_graph/breakpoint_graph.py
+index c9aa6c2..e73afd9 100644
+--- a/ragout/breakpoint_graph/breakpoint_graph.py
++++ b/ragout/breakpoint_graph/breakpoint_graph.py
+@@ -272,7 +272,7 @@ def _output_graph(graph, out_file):
+ """
+ with open(out_file, "w") as fout:
+ fout.write("graph {\n")
+- for v1, v2, data in graph.edges_iter(data=True):
++ for v1, v2, data in graph.edges(data=True):
+ fout.write("{0} -- {1}".format(v1, v2))
+ if len(data):
+ extra = list(map(lambda (k, v) : "{0}=\"{1}\"".format(k, v),
+diff --git a/ragout/breakpoint_graph/chimera_detector.py b/ragout/breakpoint_graph/chimera_detector.py
+index d72440f..06b8f08 100644
+--- a/ragout/breakpoint_graph/chimera_detector.py
++++ b/ragout/breakpoint_graph/chimera_detector.py
+@@ -98,7 +98,7 @@ def _get_contig_breaks(self, bp_graph):
+ logger.debug("Processing component of size {0}"
+ .format(len(subgr.bp_graph)))
+
+- for (u, v, data) in subgr.bp_graph.edges_iter(data=True):
++ for (u, v, data) in subgr.bp_graph.edges(data=True):
+ if data["genome_id"] != subgr.target:
+ continue
+
+diff --git a/ragout/breakpoint_graph/inferer.py b/ragout/breakpoint_graph/inferer.py
+index a2c8134..7cdc5c3 100644
+--- a/ragout/breakpoint_graph/inferer.py
++++ b/ragout/breakpoint_graph/inferer.py
+@@ -115,7 +115,7 @@ def _trim_known_edges(self, graph):
+ Removes edges with known target adjacencies (red edges from paper)
+ """
+ trimmed_graph = graph.copy()
+- for v1, v2 in graph.edges_iter():
++ for v1, v2 in graph.edges():
+ if not trimmed_graph.has_node(v1) or not trimmed_graph.has_node(v2):
+ continue
+
+@@ -142,7 +142,7 @@ def _min_weight_matching(graph):
+ """
+ Finds a perfect matching with minimum weight
+ """
+- for v1, v2 in graph.edges_iter():
++ for v1, v2 in graph.edges():
+ graph[v1][v2]["weight"] = -graph[v1][v2]["weight"] #want minimum weght
+
+ MIN_LOG_SIZE = 20
+diff --git a/ragout/scaffolder/merge_iters.py b/ragout/scaffolder/merge_iters.py
+index fd6c9cd..66be623 100644
+--- a/ragout/scaffolder/merge_iters.py
++++ b/ragout/scaffolder/merge_iters.py
+@@ -179,7 +179,7 @@ def project(self):
+
+ red_edges = []
+ black_edges = []
+- for (u, v, data) in subgr.edges_iter(data=True):
++ for (u, v, data) in subgr.edges(data=True):
+ if data["scf_set"] == "old":
+ red_edges.append((u, v))
+ else:
+@@ -201,7 +201,7 @@ def project(self):
+
+ logger.debug("Made {0} k-breaks".format(num_kbreaks))
+ adjacencies = {}
+- for (u, v, data) in self.bp_graph.edges_iter(data=True):
++ for (u, v, data) in self.bp_graph.edges(data=True):
+ if data["scf_set"] == "old":
+ gap, support = 0, []
+ if not data["infinity"]:
+diff --git a/scripts/debug-report.py b/scripts/debug-report.py
+index 017d3c8..e118f46 100755
+--- a/scripts/debug-report.py
++++ b/scripts/debug-report.py
+@@ -113,11 +113,11 @@ def compose_breakpoint_graph(base_dot, predicted_dot, true_edges):
+ predicted_edges = nx.read_dot(predicted_dot)
+ out_graph = nx.MultiGraph()
+
+- for v1, v2, data in base_graph.edges_iter(data=True):
++ for v1, v2, data in base_graph.edges(data=True):
+ color = g2c(data["genome_id"])
+ label = "oo" if data["infinity"] == "True" else ""
+ out_graph.add_edge(v1, v2, color=color, label=label)
+- for v1, v2 in predicted_edges.edges_iter():
++ for v1, v2 in predicted_edges.edges():
+ out_graph.add_edge(v1, v2, color="red", style="dashed")
+ for (v1, v2, infinite) in true_edges:
+ label = "oo" if infinite else ""
+@@ -140,7 +140,7 @@ def output_graph(graph, output_dir, only_predicted):
+
+ if only_predicted:
+ to_show = False
+- for v1, v2, data in subgr.edges_iter(data=True):
++ for v1, v2, data in subgr.edges(data=True):
+ if data.get("style") == "dashed":
+ to_show = True
+ break
=====================================
debian/patches/e3a06ef1256cf132903bbf19c9d4e11ea846e6df.patch
=====================================
@@ -0,0 +1,32 @@
+From e3a06ef1256cf132903bbf19c9d4e11ea846e6df Mon Sep 17 00:00:00 2001
+From: Tatiana Malygina <merlettaia at gmail.com>
+Date: Mon, 25 Mar 2019 16:19:40 +0300
+Origin: https://github.com/fenderglass/Ragout/pull/41
+Subject: [PATCH] fix TypeError: object of type 'dictionary-keyiterator' has no
+ len()
+
+---
+ ragout/scaffolder/merge_iters.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/ragout/scaffolder/merge_iters.py b/ragout/scaffolder/merge_iters.py
+index 66be623..3536f5c 100644
+--- a/ragout/scaffolder/merge_iters.py
++++ b/ragout/scaffolder/merge_iters.py
+@@ -174,7 +174,7 @@ def project(self):
+ subgraphs = list(nx.connected_component_subgraphs(self.bp_graph))
+ for subgr in subgraphs:
+ #this is a cycle
+- if any(len(subgr.neighbors(node)) != 2 for node in subgr.nodes()):
++ if any(len(subgr[node]) != 2 for node in subgr.nodes()):
+ continue
+
+ red_edges = []
+@@ -193,6 +193,7 @@ def project(self):
+ self.bp_graph.remove_edge(u, v)
+ self.adj_graph.remove_edge(u, v)
+ for u, v in black_edges:
++ print(self.bp_graph[u][v])
+ link = self.bp_graph[u][v][0]["link"]
+ infinity = self.bp_graph[u][v][0]["infinity"]
+ self.bp_graph.add_edge(u, v, scf_set="old",
=====================================
debian/patches/f4d4e2223a337abdbc5873fd6560e1494e55342d.patch
=====================================
@@ -0,0 +1,37 @@
+From f4d4e2223a337abdbc5873fd6560e1494e55342d Mon Sep 17 00:00:00 2001
+From: Tatiana Malygina <merlettaia at gmail.com>
+Date: Mon, 25 Mar 2019 17:08:08 +0300
+Origin: https://github.com/fenderglass/Ragout/pull/41
+Subject: [PATCH] fix AttributeError: 'set' object has no attribute 'items'
+
+---
+ ragout/breakpoint_graph/inferer.py | 2 +-
+ ragout/breakpoint_graph/repeat_resolver.py | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/ragout/breakpoint_graph/inferer.py b/ragout/breakpoint_graph/inferer.py
+index 7cdc5c3..eb47032 100644
+--- a/ragout/breakpoint_graph/inferer.py
++++ b/ragout/breakpoint_graph/inferer.py
+@@ -151,7 +151,7 @@ def _min_weight_matching(graph):
+ "size {0}".format(len(graph)))
+ edges = nx.max_weight_matching(graph, maxcardinality=True)
+ unique_edges = set()
+- for v1, v2 in edges.items():
++ for v1, v2 in edges:
+ if not (v2, v1) in unique_edges:
+ unique_edges.add((v1, v2))
+
+diff --git a/ragout/breakpoint_graph/repeat_resolver.py b/ragout/breakpoint_graph/repeat_resolver.py
+index b3054e5..a20ea11 100644
+--- a/ragout/breakpoint_graph/repeat_resolver.py
++++ b/ragout/breakpoint_graph/repeat_resolver.py
+@@ -362,7 +362,7 @@ def _profile_similarity(profile, genome_ctx, repeats, same_len):
+ def _max_weight_matching(graph):
+ edges = nx.max_weight_matching(graph, maxcardinality=True)
+ unique_edges = set()
+- for v1, v2 in edges.items():
++ for v1, v2 in edges:
+ if not (v2, v1) in unique_edges:
+ unique_edges.add((v1, v2))
+
=====================================
debian/patches/series
=====================================
@@ -1 +1,4 @@
install_newick.patch
+d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0.patch
+e3a06ef1256cf132903bbf19c9d4e11ea846e6df.patch
+f4d4e2223a337abdbc5873fd6560e1494e55342d.patch
View it on GitLab: https://salsa.debian.org/med-team/ragout/compare/b1fcb230f6b4dc696c1d4aa8111f0a625024aab6...12f1dde8dd02069244aa52de0301ec180c09af98
--
View it on GitLab: https://salsa.debian.org/med-team/ragout/compare/b1fcb230f6b4dc696c1d4aa8111f0a625024aab6...12f1dde8dd02069244aa52de0301ec180c09af98
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