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

+From d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0 Mon Sep 17 00:00:00 2001
+From: Tatiana Malygina <merlettaia@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

+From e3a06ef1256cf132903bbf19c9d4e11ea846e6df Mon Sep 17 00:00:00 2001
+From: Tatiana Malygina <merlettaia@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

+From f4d4e2223a337abdbc5873fd6560e1494e55342d Mon Sep 17 00:00:00 2001
+From: Tatiana Malygina <merlettaia@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

 install_newick.patch
+d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0.patch
+e3a06ef1256cf132903bbf19c9d4e11ea846e6df.patch
+f4d4e2223a337abdbc5873fd6560e1494e55342d.patch