[med-svn] [Git][med-team/hinge][master] 6 commits: Add myself to Uploaders
Andreas Tille
gitlab at salsa.debian.org
Wed Sep 4 16:19:52 BST 2019
Andreas Tille pushed to branch master at Debian Med / hinge
Commits:
3a52b907 by Andreas Tille at 2019-09-04T14:50:32Z
Add myself to Uploaders
- - - - -
489d4d15 by Andreas Tille at 2019-09-04T15:05:05Z
Use 2to3 to port to Python3
- - - - -
8e4cd07d by Andreas Tille at 2019-09-04T15:05:25Z
debhelper-compat 12
- - - - -
c13f0c01 by Andreas Tille at 2019-09-04T15:05:29Z
Standards-Version: 4.4.0
- - - - -
713d7020 by Andreas Tille at 2019-09-04T15:17:14Z
There is no python3-configparser and it should not be needed
- - - - -
b21be0ee by Andreas Tille at 2019-09-04T15:18:56Z
TODO: Wait for python3-pbcore (see #938009)
- - - - -
5 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+hinge (0.5.0-5) UNRELEASED; urgency=medium
+
+ * Afif removed himself from Uploaders
+ * Add myself to Uploaders
+ * Use 2to3 to port to Python3
+ Closes: #936704
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ TODO: Wait for python3-pbcore (see #938009)
+
+ -- Andreas Tille <tille at debian.org> Wed, 04 Sep 2019 16:50:08 +0200
+
hinge (0.5.0-4) unstable; urgency=medium
* Team upload.
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-12
=====================================
debian/control
=====================================
@@ -1,8 +1,9 @@
Source: hinge
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
cmake,
libspdlog-dev,
libboost-dev,
@@ -12,18 +13,17 @@ Build-Depends: debhelper (>= 12~),
pandoc,
# Run-Time-Depends:
# (to prevent building where not installable)
- python,
+ python3,
daligner,
dazzdb,
dascrubber,
- python-numpy,
- python-ujson,
- python-configparser,
- python-colormap,
- python-pbcore,
- python-networkx,
- python-matplotlib
-Standards-Version: 4.3.0
+ python3-numpy,
+ python3-ujson,
+ python3-colormap,
+ python3-pbcore,
+ python3-networkx,
+ python3-matplotlib
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/hinge
Vcs-Git: https://salsa.debian.org/med-team/hinge.git
Homepage: https://github.com/HingeAssembler/HINGE
@@ -32,17 +32,16 @@ Package: hinge
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- python,
+ python3,
daligner,
dazzdb,
dascrubber,
- python-numpy,
- python-ujson,
- python-configparser,
- python-colormap,
- python-pbcore,
- python-networkx,
- python-matplotlib
+ python3-numpy,
+ python3-ujson,
+ python3-colormap,
+ python3-pbcore,
+ python3-networkx,
+ python3-matplotlib
Description: long read genome assembler based on hinging
HINGE is a genome assembler that seeks to achieve optimal repeat resolution
by distinguishing repeats that can be resolved given the data from those that
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,2955 @@
+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/936704
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 04 Sep 2019 16:50:08 +0200
+
+--- a/README.md
++++ b/README.md
+@@ -5,7 +5,7 @@ Software accompanying "HINGE: Long-Read
+
+ - Paper: http://genome.cshlp.org/content/early/2017/03/20/gr.216465.116.abstract
+
+-- An ipython notebook to reproduce results in the paper can be found in this [repository](https://github.com/govinda-kamath/HINGE-analyses).
++- An ipython3 notebook to reproduce results in the paper can be found in this [repository](https://github.com/govinda-kamath/HINGE-analyses).
+
+ CI Status: 
+
+@@ -59,9 +59,9 @@ In the pipeline described above, several
+ - cmake 3.x
+ - libhdf5
+ - boost
+-- Python 2.7
++- Python 3
+
+-The following python packages are necessary:
++The following python3 packages are necessary:
+ - numpy
+ - ujson
+ - configparser
+--- a/scripts/Visualise_graph.py
++++ b/scripts/Visualise_graph.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ # In[1]:
+
+@@ -7,7 +7,7 @@ import sys
+
+ # In[2]:
+ if len(sys.argv) >2:
+- print "wrong usage.\n python Visualise_graph.py graph_edge_file [list_of_hinges]"
++ print("wrong usage.\n python3 Visualise_graph.py graph_edge_file [list_of_hinges]")
+
+ vertices=set()
+ with open (sys.argv[1]) as f:
+@@ -40,7 +40,7 @@ for vertex in vertices:
+ with open (sys.argv[1]) as f:
+ for lines in f:
+ lines1=lines.split()
+- print lines1
++ print(lines1)
+ if len(lines1) < 5:
+ continue
+ #print lines1
+--- a/scripts/add_groundtruth.py
++++ b/scripts/add_groundtruth.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import sys
+@@ -13,20 +13,20 @@ except:
+
+ g = nx.read_graphml(graphml_file)
+
+-print nx.info(g)
++print(nx.info(g))
+
+ mapping_dict = {}
+
+ with open(groundtruth_file,'r') as f:
+ for num, line in enumerate(f.readlines()):
+- m = map(int, line.strip().split())
++ m = list(map(int, line.strip().split()))
+ # mapping_dict[num] = [min(m), max(m), int(m[0]>m[1])]
+ mapping_dict[num] = [m[2],m[3],m[1]]
+
+ #print mapping_dict
+
+ max_len=0
+-for num in mapping_dict.keys():
++for num in list(mapping_dict.keys()):
+ max_len=max(max_len,len(str(m[3])))
+
+
+--- a/scripts/add_groundtruth_json.py
++++ b/scripts/add_groundtruth_json.py
+@@ -8,7 +8,7 @@ graphml_file_w_groundtruth = sys.argv[3]
+
+ g = nx.read_graphml(graphml_file)
+
+-print nx.info(g)
++print(nx.info(g))
+
+ with open(groundtruth_file) as f:
+ read_dict=json.load(f)
+@@ -20,7 +20,7 @@ for read in read_dict:
+ max_len=max(max_len,len(str(aln_info[0])))
+ max_len=max(max_len,len(str(aln_info[1])))
+ except:
+- print
++ print()
+ raise
+
+ pow_mov=10**(max_len+1)
+--- a/scripts/clip_ends.py
++++ b/scripts/clip_ends.py
+@@ -8,7 +8,7 @@ out_file=sys.argv[2]+'.clipped'
+
+ with open(ground_truth) as f:
+ for line in f:
+- m = map(int, line.strip().split())
++ m = list(map(int, line.strip().split()))
+ chr_lengths.setdefault(m[1],0)
+ chr_lengths[m[1]]= max(chr_lengths[m[1]], max(m[2],m[3]))
+
+@@ -18,7 +18,7 @@ reads_to_kill=set()
+
+ with open(ground_truth) as f:
+ for line in f:
+- m = map(int, line.strip().split())
++ m = list(map(int, line.strip().split()))
+ read_left=min(m[2],m[3])
+ read_right=max(m[2],m[3])
+ read_chr=m[1]
+--- a/scripts/compute_n50_from_draft.py
++++ b/scripts/compute_n50_from_draft.py
+@@ -119,9 +119,9 @@ for nctc_name in os.listdir(fullpath):
+
+ data_dict[nctc_name] = [hinging_n50,hinging_comp_n50,hgap_n50]
+
+- print count
+- print count1
+- print count2
++ print(count)
++ print(count1)
++ print(count2)
+
+
+
+--- a/scripts/condense_graph.py
++++ b/scripts/condense_graph.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import sys
+@@ -90,7 +90,7 @@ def run(filename, n_iter):
+
+ f=open(filename)
+ line1=f.readline()
+- print line1
++ print(line1)
+ f.close()
+ if len(line1.split()) !=2:
+ g=input1(filename)
+@@ -99,7 +99,7 @@ def run(filename, n_iter):
+
+
+
+- print nx.info(g)
++ print(nx.info(g))
+
+
+ for node in g.nodes():
+@@ -107,37 +107,37 @@ def run(filename, n_iter):
+ g.node[node]['read'] = node
+
+
+- degree_sequence=sorted(g.degree().values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(g.degree().values()),reverse=True)
++ print(Counter(degree_sequence))
+ for i in range(n_iter):
+ for node in g.nodes():
+ if g.in_degree(node) == 0:
+ g.remove_node(node)
+
+- print nx.info(g)
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ print(nx.info(g))
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+
+ g.graph['aval'] = 1000000000
+
+ for i in range(5):
+ merge_simple_path(g)
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+ try:
+ import ujson
+ mapping = ujson.load(open(filename.split('.')[0]+'.mapping.json'))
+
+- print 'get mapping'
++ print('get mapping')
+
+ for node in g.nodes():
+ #print node
+- if mapping.has_key(node):
++ if node in mapping:
+ g.node[node]['aln_start'] = mapping[node][0]
+ g.node[node]['aln_end'] = mapping[node][1]
+ g.node[node]['aln_strand'] = mapping[node][2]
+@@ -151,8 +151,8 @@ def run(filename, n_iter):
+
+ nx.write_graphml(g, filename.split('.')[0]+'_condensed.graphml')
+
+- print nx.number_weakly_connected_components(g)
+- print nx.number_strongly_connected_components(g)
++ print(nx.number_weakly_connected_components(g))
++ print(nx.number_strongly_connected_components(g))
+
+
+ filename = sys.argv[1]
+--- a/scripts/condense_graph_and_annotate.py
++++ b/scripts/condense_graph_and_annotate.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import sys
+@@ -94,21 +94,21 @@ def run(filename, gt_file, n_iter):
+
+ f=open(filename)
+ line1=f.readline()
+- print line1
++ print(line1)
+ f.close()
+ if len(line1.split()) !=2:
+ g=input1(filename)
+ else:
+ g=input2(filename)
+
+- print str(len(g.nodes())) + " vertices in graph to begin with."
++ print(str(len(g.nodes())) + " vertices in graph to begin with.")
+
+ connected_components=[x for x in nx.weakly_connected_components(g)]
+ for component in connected_components:
+ if len(component) < 10:
+ g.remove_nodes_from(component)
+
+- print str(len(g.nodes())) + " vertices in graph after removing components of at most "+str(LENGTH_THRESHOLD)+ " nodes."
++ print(str(len(g.nodes())) + " vertices in graph after removing components of at most "+str(LENGTH_THRESHOLD)+ " nodes.")
+
+ read_to_chr_map={}
+
+@@ -121,7 +121,7 @@ def run(filename, gt_file, n_iter):
+ else:
+ with open(gt_file,'r') as f:
+ for num, line in enumerate(f.readlines()):
+- m = map(int, line.strip().split())
++ m = list(map(int, line.strip().split()))
+ read_to_chr_map[m[0]]=m[1]
+
+ nodes_seen=set([x.split("_")[0] for x in g.nodes()])
+@@ -130,7 +130,7 @@ def run(filename, gt_file, n_iter):
+ read_to_chr_map.setdefault(int(node),-1)
+
+ #print nx.info(g)
+- print "Num reads read : "+str(len(read_to_chr_map))
++ print("Num reads read : "+str(len(read_to_chr_map)))
+
+ for node in g.nodes():
+ nodeid=int(node.split('_')[0])
+@@ -140,27 +140,27 @@ def run(filename, gt_file, n_iter):
+ #print str(nodeid), node,g.node[node]['chr']
+
+
+- degree_sequence=sorted(g.degree().values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(g.degree().values()),reverse=True)
++ print(Counter(degree_sequence))
+ for i in range(n_iter):
+ for node in g.nodes():
+ if g.in_degree(node) == 0:
+ g.remove_node(node)
+
+- print nx.info(g)
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ print(nx.info(g))
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+
+ g.graph['aval'] = 1000000000
+
+ for i in range(5):
+ merge_simple_path(g)
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+ h=nx.DiGraph()
+ h.add_nodes_from(g)
+@@ -168,9 +168,9 @@ def run(filename, gt_file, n_iter):
+ for node in g.nodes():
+ reads_in_node=[int(x.split('_')[0]) for x in g.node[node]['read'].split(':')]
+ try:
+- chr_in_node=map(lambda x: read_to_chr_map[x], reads_in_node)
++ chr_in_node=[read_to_chr_map[x] for x in reads_in_node]
+ except:
+- print reads_in_node,g.node[node]['read']
++ print(reads_in_node,g.node[node]['read'])
+ return
+ chr_in_node_set=set(chr_in_node)
+ if len(chr_in_node_set) ==1:
+@@ -187,8 +187,8 @@ def run(filename, gt_file, n_iter):
+
+ nx.write_graphml(h, filename.split('.')[0]+'_condensed_annotated.graphml')
+
+- print nx.number_weakly_connected_components(h)
+- print nx.number_strongly_connected_components(h)
++ print(nx.number_weakly_connected_components(h))
++ print(nx.number_strongly_connected_components(h))
+
+ #
+
+--- a/scripts/condense_graph_annotate_clip_ends.py
++++ b/scripts/condense_graph_annotate_clip_ends.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import sys
+@@ -93,7 +93,7 @@ def run(filename, gt_file, n_iter):
+
+ f=open(filename)
+ line1=f.readline()
+- print line1
++ print(line1)
+ f.close()
+ if len(line1.split()) !=2:
+ g=input1(filename)
+@@ -110,7 +110,7 @@ def run(filename, gt_file, n_iter):
+
+ with open(gt_file,'r') as f:
+ for num, line in enumerate(f.readlines()):
+- m = map(int, line.strip().split())
++ m = list(map(int, line.strip().split()))
+ # mapping_dict[num] = [min(m), max(m), int(m[0]>m[1])]
+ read_to_chr_map[m[0]]= str(m[1])
+ mapping_dict[num] = m[1]
+@@ -119,10 +119,10 @@ def run(filename, gt_file, n_iter):
+ chr_lengths[m[1]] = max(chr_lengths[m[1]],max(m[2],m[3]))
+
+
+- print nx.info(g)
++ print(nx.info(g))
+
+- print "Chromosome lenghts:"
+- print chr_lengths
++ print("Chromosome lenghts:")
++ print(chr_lengths)
+
+ margin = 10000
+
+@@ -130,7 +130,7 @@ def run(filename, gt_file, n_iter):
+
+
+ #print nx.info(g)
+- print "Num reads read : "+str(len(read_to_chr_map))
++ print("Num reads read : "+str(len(read_to_chr_map)))
+
+ for cur_edge in g.edges():
+ node0=int(cur_edge[0].split('_')[0])
+@@ -162,30 +162,30 @@ def run(filename, gt_file, n_iter):
+ g.node[node]['read'] = node
+ #print str(nodeid), node,g.node[node]['chr']
+
+- print "Deleted nodes: "+str(del_count)
++ print("Deleted nodes: "+str(del_count))
+
+
+- degree_sequence=sorted(g.degree().values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(g.degree().values()),reverse=True)
++ print(Counter(degree_sequence))
+ for i in range(n_iter):
+ for node in g.nodes():
+ if g.in_degree(node) == 0:
+ g.remove_node(node)
+
+- print nx.info(g)
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ print(nx.info(g))
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+
+ g.graph['aval'] = 1000000000
+
+ for i in range(5):
+ merge_simple_path(g)
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+ h=nx.DiGraph()
+ h.add_nodes_from(g)
+@@ -200,9 +200,9 @@ def run(filename, gt_file, n_iter):
+ for node in g.nodes():
+ reads_in_node=[int(x.split('_')[0]) for x in g.node[node]['read'].split(':')]
+ try:
+- chr_in_node=map(lambda x: read_to_chr_map[x], reads_in_node)
++ chr_in_node=[read_to_chr_map[x] for x in reads_in_node]
+ except:
+- print reads_in_node,g.node[node]['read']
++ print(reads_in_node,g.node[node]['read'])
+ return
+ chr_in_node_set=set(chr_in_node)
+ if len(chr_in_node_set) ==1:
+@@ -221,11 +221,11 @@ def run(filename, gt_file, n_iter):
+ import ujson
+ mapping = ujson.load(open(filename.split('.')[0]+'.mapping.json'))
+
+- print 'get mapping'
++ print('get mapping')
+
+ for node in h.nodes():
+ #print node
+- if mapping.has_key(node):
++ if node in mapping:
+ h.node[node]['aln_start'] = mapping[node][0]
+ h.node[node]['aln_end'] = mapping[node][1]
+ h.node[node]['aln_strand'] = mapping[node][2]
+@@ -242,8 +242,8 @@ def run(filename, gt_file, n_iter):
+ nx.write_graphml(h, filename.split('.')[0]+'_condensed_annotated.graphml')
+ nx.write_graphml(g, filename.split('.')[0]+'_G_condensed_annotated.graphml')
+
+- print nx.number_weakly_connected_components(h)
+- print nx.number_strongly_connected_components(h)
++ print(nx.number_weakly_connected_components(h))
++ print(nx.number_strongly_connected_components(h))
+
+ #
+
+--- a/scripts/condense_graph_create_gfa_compute_n50.py
++++ b/scripts/condense_graph_create_gfa_compute_n50.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import sys
+@@ -7,7 +7,7 @@ from collections import Counter
+
+ # This script condenses the graph down, creates a gfa with for the condensed graph, and computes the contig N50
+
+-# python condense_graph_create_gfa_compute_n50.py ecoli.edges
++# python3 condense_graph_create_gfa_compute_n50.py ecoli.edges
+
+ # The conditions in lines 23 and 24 are meant to prevent nodes corresponding to different strands to be merged
+ # (and should be commented out if this is not desired, or if a json is not available)
+@@ -46,8 +46,8 @@ def merge_path(g,in_node,node,out_node):
+
+
+ if overlap1 > min(length0,length1):
+- print "problem here:"
+- print overlap1, length0, length1
++ print("problem here:")
++ print(overlap1, length0, length1)
+
+
+ g.add_node(str(node_id),length = length0+length1+length2 - overlap1 - overlap2, aln_strand = g.node[node]['aln_strand'])
+@@ -107,7 +107,7 @@ def de_clip(filename, n_iter):
+ # count = 0
+
+ with open(filename,'r') as f:
+- for line in f.xreadlines():
++ for line in f:
+ l = line.strip().split()
+ #print l2
+ g.add_edge(l[0],l[1],overlap=int(l[2])/2)
+@@ -126,7 +126,7 @@ def de_clip(filename, n_iter):
+ g.node[l[1]]['length'] = node1end - node1start
+
+
+- print nx.info(g)
++ print(nx.info(g))
+
+ try:
+ import ujson
+@@ -134,11 +134,11 @@ def de_clip(filename, n_iter):
+
+ # print mapping
+
+- print 'get mapping'
++ print('get mapping')
+
+ for node in g.nodes():
+ #print node
+- if mapping.has_key(node):
++ if node in mapping:
+
+ # alnstart = int(mapping[node][0])
+ # alnend = int(mapping[node][1])
+@@ -164,34 +164,34 @@ def de_clip(filename, n_iter):
+
+
+
+- degree_sequence=sorted(g.degree().values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(g.degree().values()),reverse=True)
++ print(Counter(degree_sequence))
+ for i in range(n_iter):
+ for node in g.nodes():
+ if g.degree(node) < 2:
+ g.remove_node(node)
+
+- print nx.info(g)
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ print(nx.info(g))
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+
+ g.graph['aval'] = 1000000000
+
+ for i in range(5):
+ merge_simple_path(g)
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+
+
+ nx.write_graphml(g, filename.split('.')[0]+'.graphml')
+
+- print nx.number_weakly_connected_components(g)
+- print nx.number_strongly_connected_components(g)
++ print(nx.number_weakly_connected_components(g))
++ print(nx.number_strongly_connected_components(g))
+
+
+ # Next we create the gfa file
+@@ -223,7 +223,7 @@ def de_clip(filename, n_iter):
+ for cur_node in g.nodes():
+ contig_lengths.append(g.node[cur_node]['length'])
+
+- print "N50 = "+str(comp_n50(contig_lengths))
++ print("N50 = "+str(comp_n50(contig_lengths)))
+
+
+
+--- a/scripts/condense_graph_with_gt.py
++++ b/scripts/condense_graph_with_gt.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import sys
+@@ -96,7 +96,7 @@ def run(filename, gt_file, n_iter):
+
+ f=open(filename)
+ line1=f.readline()
+- print line1
++ print(line1)
+ f.close()
+ if len(line1.split()) !=2:
+ g=input1(filename)
+@@ -107,11 +107,11 @@ def run(filename, gt_file, n_iter):
+
+ with open(gt_file,'r') as f:
+ for num, line in enumerate(f.readlines()):
+- m = map(int, line.strip().split())
++ m = list(map(int, line.strip().split()))
+ # mapping_dict[num] = [min(m), max(m), int(m[0]>m[1])]
+ mapping_dict[num] = m[1]
+
+- print nx.info(g)
++ print(nx.info(g))
+
+
+ for node in g.nodes():
+@@ -123,27 +123,27 @@ def run(filename, gt_file, n_iter):
+ #print str(nodeid), node,g.node[node]['chr']
+
+
+- degree_sequence=sorted(g.degree().values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(g.degree().values()),reverse=True)
++ print(Counter(degree_sequence))
+ for i in range(n_iter):
+ for node in g.nodes():
+ if g.in_degree(node) == 0:
+ g.remove_node(node)
+
+- print nx.info(g)
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ print(nx.info(g))
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+
+ g.graph['aval'] = 1000000000
+
+ for i in range(5):
+ merge_simple_path(g)
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+ h=nx.DiGraph()
+ h.add_nodes_from(g)
+@@ -161,11 +161,11 @@ def run(filename, gt_file, n_iter):
+ import ujson
+ mapping = ujson.load(open(filename.split('.')[0]+'.mapping.json'))
+
+- print 'get mapping'
++ print('get mapping')
+
+ for node in h.nodes():
+ #print node
+- if mapping.has_key(node):
++ if node in mapping:
+ h.node[node]['aln_start'] = mapping[node][0]
+ h.node[node]['aln_end'] = mapping[node][1]
+ h.node[node]['aln_strand'] = mapping[node][2]
+@@ -181,8 +181,8 @@ def run(filename, gt_file, n_iter):
+
+ nx.write_graphml(h, filename.split('.')[0]+'_condensed.graphml')
+
+- print nx.number_weakly_connected_components(h)
+- print nx.number_strongly_connected_components(h)
++ print(nx.number_weakly_connected_components(h))
++ print(nx.number_strongly_connected_components(h))
+
+ #
+
+--- a/scripts/connected.py
++++ b/scripts/connected.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import sys
+@@ -13,7 +13,7 @@ def longest_path(G):
+ dist[node] = max(pairs)
+ else:
+ dist[node] = (0, node)
+- node,(length,_) = max(dist.items(), key=lambda x:x[1])
++ node,(length,_) = max(list(dist.items()), key=lambda x:x[1])
+ path = []
+ while length > 0:
+ path.append(node)
+@@ -27,25 +27,25 @@ filename = sys.argv[1]
+ g = nx.DiGraph()
+
+ with open(filename,'r') as f:
+- for line in f.xreadlines():
++ for line in f:
+ g.add_edge(*(line.strip().split('->')))
+
+
+-print nx.info(g)
+-degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+-print Counter(degree_sequence)
++print(nx.info(g))
++degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++print(Counter(degree_sequence))
+
+ for i in range(15):
+ for node in g.nodes():
+ if g.in_degree(node) == 0:
+ g.remove_node(node)
+
+- print nx.info(g)
++ print(nx.info(g))
+
+ #print nx.is_directed_acyclic_graph(g)
+ #print list(nx.simple_cycles(g))
+-degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+-print Counter(degree_sequence)
++degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++print(Counter(degree_sequence))
+
+ #print nx.diameter(g)
+
+@@ -60,8 +60,8 @@ def rev(string):
+ #print edge
+ #print rev(edge[1]), rev(edge[0])
+
+-print nx.info(g)
+-print [len(item) for item in nx.weakly_connected_components(g)]
++print(nx.info(g))
++print([len(item) for item in nx.weakly_connected_components(g)])
+
+
+ nx.write_graphml(g, filename.split('.')[0]+'.graphml')
+--- a/scripts/correct_head.py
++++ b/scripts/correct_head.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys, os
+ from pbcore.io import FastaIO
+--- a/scripts/create_bandage_file.py
++++ b/scripts/create_bandage_file.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+ import os
+--- a/scripts/create_hgraph.py
++++ b/scripts/create_hgraph.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import random
+@@ -42,8 +42,8 @@ def read_graph(filename,gt_file):
+
+ nx.write_graphml(g, filename.split('.')[0]+'_hgraph.graphml')
+
+- print nx.number_weakly_connected_components(g)
+- print nx.number_strongly_connected_components(g)
++ print(nx.number_weakly_connected_components(g))
++ print(nx.number_strongly_connected_components(g))
+
+
+ if __name__ == "__main__":
+--- a/scripts/create_hgraph_nogt.py
++++ b/scripts/create_hgraph_nogt.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import random
+@@ -28,8 +28,8 @@ def read_graph(filename):
+
+ nx.write_graphml(g, filename.split('.')[0]+'_hgraph.graphml')
+
+- print nx.number_weakly_connected_components(g)
+- print nx.number_strongly_connected_components(g)
++ print(nx.number_weakly_connected_components(g))
++ print(nx.number_strongly_connected_components(g))
+
+
+ if __name__ == "__main__":
+--- a/scripts/download_NCTC_pipeline.py
++++ b/scripts/download_NCTC_pipeline.py
+@@ -20,10 +20,10 @@ dest_dir = base_dir+bacterium_of_interes
+
+ os.system('mkdir -p '+dest_dir)
+
+-for run, file_list in bact_dict[bacterium_of_interest]['file_paths'].items():
++for run, file_list in list(bact_dict[bacterium_of_interest]['file_paths'].items()):
+ for file_path in file_list:
+ cmd = cmd_base+file_path+' '+dest_dir
+- print cmd
++ print(cmd)
+ os.system(cmd)
+
+ dest_fasta_name = dest_dir+bact_name
+@@ -35,16 +35,16 @@ bax_files = [x for x in os.listdir(dest_
+ for bax_file in bax_files:
+ dextract_cmd += " " + dest_dir+bax_file
+
+-print dextract_cmd
++print(dextract_cmd)
+
+ try:
+ subprocess.check_output(dextract_cmd.split())
+- print 'dextract done. deleting .bax.h5 files'
++ print('dextract done. deleting .bax.h5 files')
+ os.system('rm '+dest_dir+'*.bax.h5')
+- print 'removing .quiva files'
++ print('removing .quiva files')
+ os.system('rm '+dest_dir+'*.quiva')
+ except:
+- print 'error'
++ print('error')
+
+
+
+--- a/scripts/draft_assembly.py
++++ b/scripts/draft_assembly.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import sys
+@@ -8,16 +8,16 @@ def linearize(filename):
+ graph_name = filename.split('.')[0]+'.graphml'
+ g = nx.read_graphml(graph_name)
+
+- print nx.info(g)
++ print(nx.info(g))
+
+ # get first strong connected component
+
+ con = list(nx.strongly_connected_component_subgraphs(g))
+
+ con.sort(key = lambda x:len(x), reverse = True)
+- print [len(item) for item in con]
++ print([len(item) for item in con])
+
+- print nx.info(con[0])
++ print(nx.info(con[0]))
+
+ dfs_edges = list(nx.dfs_edges(con[0]))
+
+--- a/scripts/draft_assembly_not_perfect.py
++++ b/scripts/draft_assembly_not_perfect.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import sys
+@@ -8,16 +8,16 @@ def linearize(filename):
+ graph_name = filename.split('.')[0]+'.graphml'
+ g = nx.read_graphml(graph_name)
+
+- print nx.info(g)
++ print(nx.info(g))
+
+ # get first strong connected component
+
+ con = list(nx.strongly_connected_component_subgraphs(g))
+
+ con.sort(key = lambda x:len(x), reverse = True)
+- print [len(item) for item in con]
++ print([len(item) for item in con])
+
+- print nx.info(con[0])
++ print(nx.info(con[0]))
+
+ dfs_edges = list(nx.dfs_edges(con[0]))
+
+--- a/scripts/draw2.py
++++ b/scripts/draw2.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import numpy as np
+ import matplotlib
+ matplotlib.use('Agg')
+@@ -17,9 +17,9 @@ Qvd = ['a', 'b', 'c', 'd', 'e', 'f', 'g'
+ 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N',
+ 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X',
+ 'Y']
+-Qvv = range(len(Qvd))[::-1]
++Qvv = list(range(len(Qvd)))[::-1]
+
+-QVdict = dict(zip(Qvd,Qvv))
++QVdict = dict(list(zip(Qvd,Qvv)))
+
+
+ dbname = sys.argv[1]
+@@ -51,7 +51,7 @@ if len(sys.argv) < 7:
+ else:
+ rev = int(sys.argv[6])
+
+-print 'rev', rev
++print('rev', rev)
+
+ for i in range(len(qv)):
+ qx.append(i*ts)
+@@ -80,7 +80,7 @@ for item in aln:
+ aln_group.append(item)
+
+ num = len(alns)
+-print len(aln), len(alns)
++print(len(aln), len(alns))
+
+ #print [len(item) for item in alns]
+ #print [item[0:3] for item in aln]
+--- a/scripts/draw2_pileup.py
++++ b/scripts/draw2_pileup.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import numpy as np
+ import matplotlib
+ matplotlib.use('Agg')
+@@ -30,13 +30,13 @@ path = '/data/pacbio_assembly/AwesomeAss
+ aln = []
+ for i,e in enumerate(rst):
+ n = e[0]
+- print i,n
++ print(i,n)
+ li = list(util.get_alignments_mapping(path+'ecoli', path + 'ecoli.ref', path +'ecoli.ecoli.ref.las', [n]))
+ if (len(li) > 0):
+ item = sorted(li, key=lambda x:x[4] - x[3], reverse = True)[0]
+ aln.append(item)
+
+-print aln[0:20]
++print(aln[0:20])
+
+ #aln.sort(key = lambda x:x[2])
+
+@@ -54,7 +54,7 @@ for item in aln:
+ aln_group.append(item)
+
+ num = len(alns)
+-print len(aln), len(alns)
++print(len(aln), len(alns))
+
+ #print [len(item) for item in alns]
+ #print [item[0:3] for item in aln]
+--- a/scripts/draw2_pileup_region.py
++++ b/scripts/draw2_pileup_region.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import numpy as np
+ import matplotlib
+ matplotlib.use('Agg')
+@@ -28,14 +28,14 @@ with open('ecoli.linear.edges') as f:
+
+ bb.append(int(e))
+
+-print bb
++print(bb)
+
+ bb = set(bb)
+
+
+ for i,item in enumerate(util.get_alignments_mapping2(path+'draft', path +'ecoli', path +'draft.ecoli.las')):
+ if i%2000 == 0:
+- print i, item
++ print(i, item)
+
+ if item[3] >= left and item[4] <= right:
+ aln.append(item)
+@@ -47,7 +47,7 @@ for i,item in enumerate(util.get_alignme
+
+
+
+-print 'number:',len(aln)
++print('number:',len(aln))
+ aln.sort(key = lambda x:x[2])
+
+ alns = []
+@@ -65,7 +65,7 @@ for item in aln:
+
+ num = len(alns)
+
+-print len(aln), len(alns)
++print(len(aln), len(alns))
+
+ alns.sort(key = lambda x:min([item[3] for item in x]))
+
+--- a/scripts/draw2_pileup_w_repeat.py
++++ b/scripts/draw2_pileup_w_repeat.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import numpy as np
+ import matplotlib
+ matplotlib.use('Agg')
+@@ -22,10 +22,10 @@ with open(n) as f:
+ rep = {}
+ with open(path + 'ecoli.repeat.txt') as f:
+ for line in f:
+- l = map(int, line.strip().split())
++ l = list(map(int, line.strip().split()))
+ if len(l) > 1:
+ for i in range((len(l) - 1) / 2):
+- if not rep.has_key(l[0]):
++ if l[0] not in rep:
+ rep[l[0]] = []
+ rep[l[0]].append((l[2*i+1], l[2*i+2]))
+
+@@ -34,14 +34,14 @@ with open(path + 'ecoli.repeat.txt') as
+ aln = []
+ for i,e in enumerate(rst):
+ n = e
+- print i,n
++ print(i,n)
+ li = list(util.get_alignments_mapping(path+'ecoli', path + 'ecoli.ref', path +'ecoli.ecoli.ref.las', [n]))
+ if (len(li) > 0):
+ item = sorted(li, key=lambda x:x[4] - x[3], reverse = True)
+ for l in item:
+ aln.append(l)
+
+-print aln[0:20]
++print(aln[0:20])
+
+
+ #aln.sort(key = lambda x:x[2])
+@@ -61,7 +61,7 @@ for item in aln:
+ aln_group.append(item)
+
+ num = len(alns)
+-print len(aln), len(alns)
++print(len(aln), len(alns))
+
+ #print [len(item) for item in alns]
+ #print [item[0:3] for item in aln]
+@@ -134,7 +134,7 @@ for i,aln_group in enumerate(alns):
+ # plt.gca().add_patch(polygon2)
+
+
+- if rep.has_key(rid):
++ if rid in rep:
+ for item in rep[rid]:
+ s = item[0]
+ e = item[1]
+--- a/scripts/draw_pileup_region.py
++++ b/scripts/draw_pileup_region.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import numpy as np
+ import matplotlib
+ matplotlib.use('Agg')
+@@ -39,7 +39,7 @@ aln = []
+
+ for i,item in enumerate(util.get_alignments_mapping3(ref, read, las, contig)):
+ if i%2000 == 0:
+- print i, item
++ print(i, item)
+
+ if item[3] >= left and item[4] <= right and item[4] - item[3] > length_th:
+ aln.append(item)
+@@ -53,7 +53,7 @@ for item in aln:
+ covx = np.arange(left, right)
+
+
+-print 'number:',len(aln)
++print('number:',len(aln))
+ aln.sort(key = lambda x:x[2])
+
+ alns = []
+@@ -72,7 +72,7 @@ for item in aln:
+ #num = len(alns)
+ num = len(aln)
+
+-print len(aln), len(alns)
++print(len(aln), len(alns))
+
+ alns.sort(key = lambda x:min([item[3] for item in x]))
+
+--- a/scripts/draw_pileup_region_find_bridges.py
++++ b/scripts/draw_pileup_region_find_bridges.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import numpy as np
+ import matplotlib
+ matplotlib.use('Agg')
+@@ -57,7 +57,7 @@ covx = np.arange(left, right)
+ #for i in range(0, len(covx), 10):
+ # print covx[i], covy[i]
+
+-print 'number:',len(aln)
++print('number:',len(aln))
+ aln.sort(key = lambda x:x[2])
+
+ alns = []
+@@ -75,7 +75,7 @@ for item in aln:
+
+ num = len(alns)
+
+-print len(aln), len(alns)
++print(len(aln), len(alns))
+
+ alns.sort(key = lambda x:min([item[3] for item in x]))
+
+@@ -111,7 +111,7 @@ for i,aln_group in enumerate(alns):
+ abpos = item[3]
+ aepos = item[4]
+ if abpos < bridge_begin+200 and aepos > bridge_end-200:
+- print item
++ print(item)
+ bbpos = item[6]
+ bepos = item[7]
+ blen = item[8]
+--- a/scripts/fasta_to_fastq.py
++++ b/scripts/fasta_to_fastq.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ """
+ Convert FASTA to FASTQ file with a static
+
+--- a/scripts/get_NCTC_json.py
++++ b/scripts/get_NCTC_json.py
+@@ -1,8 +1,8 @@
+-import urllib2
++import urllib.request, urllib.error, urllib.parse
+ from bs4 import BeautifulSoup
+ import json
+
+-response = urllib2.urlopen('http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/')
++response = urllib.request.urlopen('http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/')
+ html = response.read()
+
+ soup=BeautifulSoup(html)
+@@ -13,9 +13,9 @@ headings = [th.get_text() for th in tabl
+ dataset={}
+ for row in table.find_all("tr")[1:]:
+ #
+- print row
++ print(row)
+ row1= [td.get_text() for td in row.find_all("td")]
+- print row1
++ print(row1)
+ metadata={}
+ cellname=''
+ for i, td in enumerate(row.find_all("td")):
+@@ -26,7 +26,7 @@ for row in table.find_all("tr")[1:]:
+
+ if i==1:
+ cellname=td.get_text()
+- print cellname
++ print(cellname)
+
+ if i==3:
+ # print td
+@@ -46,7 +46,7 @@ for row in table.find_all("tr")[1:]:
+ list_of_files={}
+ for run in metadata[headings[3]]:
+ link_to_go=run[1]
+- response1 = urllib2.urlopen(link_to_go+"&display=xml")
++ response1 = urllib.request.urlopen(link_to_go+"&display=xml")
+ xml = response1.read()
+ xmlsoup = BeautifulSoup(xml)
+ fllist=[]
+--- a/scripts/get_consensus_gfa.py
++++ b/scripts/get_consensus_gfa.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+ import os
+@@ -71,8 +71,8 @@ h = g.subgraph(nodes_to_keep)
+ # print len(h.nodes()), len(consensus_contigs)
+ # raise
+
+-print 'Number of contigs'
+-print len(consensus_contigs), len(h.nodes())
++print('Number of contigs')
++print(len(consensus_contigs), len(h.nodes()))
+ # print [len(x) for x in consensus_contigs]
+
+
+@@ -84,7 +84,7 @@ with open(gfaname,'w') as f:
+ # print j, i
+
+ seg = consensus_contigs[i]
+- print(len(seg))
++ print((len(seg)))
+ seg_line = "S\t"+vert+"\t"+seg + '\n'
+ f.write(seg_line)
+ for edge in h.edges():
+--- a/scripts/get_draft_annotation.py
++++ b/scripts/get_draft_annotation.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import sys
+ import os
+ import subprocess
+@@ -22,7 +22,7 @@ stream = subprocess.Popen(DBshow_cmd.spl
+ stdout=subprocess.PIPE,bufsize=1)
+ reads_queried = parse_read(stream.stdout)
+ read_dict = {}
+-for read_id,read in itertools.izip(reads,reads_queried):
++for read_id,read in zip(reads,reads_queried):
+ rdlen = len(read[1])
+ # print read
+ read_dict[read_id] = read
+@@ -30,7 +30,7 @@ for read_id,read in itertools.izip(reads
+ complement = {'A':'T','C': 'G','T':'A', 'G':'C','a':'t','t':'a','c':'g','g':'c'}
+
+ def reverse_complement(string):
+- return "".join(map(lambda x:complement[x],reversed(string)))
++ return "".join([complement[x] for x in reversed(string)])
+
+ def get_string(path):
+ #print path
+@@ -53,9 +53,9 @@ def get_string(path):
+ # print read_id
+ # print read_dict[int(read_id)][str_st:str_end]
+ # print read_str
+- print 'read len',len(read_str)
++ print('read len',len(read_str))
+ ret_str += read_str
+- print len(path), len(ret_str)
++ print(len(path), len(ret_str))
+ return ret_str
+
+
+@@ -83,7 +83,7 @@ for vert in vertices_of_interest:
+ else:
+ read_end = vert_len
+ read_tuples[vert] = (read_start,read_end)
+- print read_starts, read_ends, vert
++ print(read_starts, read_ends, vert)
+
+
+ for vert in vertices_of_interest:
+@@ -131,7 +131,7 @@ vertices_used = set([x for x in h.nodes(
+ contig_no = 1
+ for start_vertex in vertices_of_interest:
+ first_out_vertices = in_graph.successors(start_vertex)
+- print start_vertex, first_out_vertices
++ print(start_vertex, first_out_vertices)
+ for vertex in first_out_vertices:
+ predecessor = start_vertex
+ start_vertex_id,start_vertex_or = start_vertex.split("_")
+@@ -263,7 +263,7 @@ while set(in_graph.nodes())-vertices_use
+ h.node[node_name]['start_read'] = path_var[0][1][0]
+ h.node[node_name]['end_read'] = path_var[-1][1][1]
+ h.node[node_name]['segment'] = get_string(cur_path)
+- print len(cur_path)
++ print(len(cur_path))
+ h.add_edges_from([(vertRC,node_name),(node_name,vertRC)])
+
+
+@@ -294,7 +294,7 @@ while True:
+ h.remove_node(vert)
+
+ for i, vert in enumerate(h.nodes()):
+- print i,len(h.node[vert]['path'])
++ print(i,len(h.node[vert]['path']))
+
+ with open(outfile, 'w') as f:
+ for i,node in enumerate(h.nodes()):
+@@ -332,7 +332,7 @@ try:
+ except:
+ pass
+ for i, vert in enumerate(h.nodes()):
+- print i,len(h.node[vert]['path']), len(h.node[vert]['segment']), len(consensus_contigs[i])
++ print(i,len(h.node[vert]['path']), len(h.node[vert]['segment']), len(consensus_contigs[i]))
+
+
+ with open(gfaname,'w') as f:
+--- a/scripts/get_draft_path.py
++++ b/scripts/get_draft_path.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+ import os
+@@ -74,7 +74,7 @@ stream = subprocess.Popen(DBshow_cmd.spl
+ stdout=subprocess.PIPE,bufsize=1)
+ reads_queried = parse_read(stream.stdout)
+ read_dict = {}
+-for read_id,read in itertools.izip(reads,reads_queried):
++for read_id,read in zip(reads,reads_queried):
+ rdlen = len(read[1])
+ # print read
+ read_dict[read_id] = read
+@@ -273,7 +273,7 @@ with open(outfile, 'w') as f:
+ # print len(node_list),len(weights_list)
+
+ if len(node_list) != len(weights_list)+1:
+- print 'Something went wrong with contig '+str(contig_no)
++ print('Something went wrong with contig '+str(contig_no))
+ continue
+
+ # printed_nodes = printed_nodes | set(node_list)
+@@ -295,7 +295,7 @@ with open(outfile, 'w') as f:
+
+ prev_contig = out_graph.predecessors(vertex)[0]
+ cut_start = out_graph.node[prev_contig]['cut_end']
+- if out_graph.node[prev_contig].has_key('path'):
++ if 'path' in out_graph.node[prev_contig]:
+ nodeA = out_graph.node[prev_contig]['path'].split(';')[-1]
+ else:
+ nodeA = prev_contig
+@@ -338,7 +338,7 @@ with open(outfile, 'w') as f:
+ cut_end = out_graph.node[next_contig]['cut_start']
+
+ nodeA = node_list[len(weights_list)]
+- if out_graph.node[next_contig].has_key('path'):
++ if 'path' in out_graph.node[next_contig]:
+ nodeB = out_graph.node[next_contig]['path'].split(';')[0]
+ else:
+ nodeB = next_contig
+@@ -374,7 +374,7 @@ with open(outfile, 'w') as f:
+ next_contig = out_graph.successors(vertex)[0]
+
+ nodeB = rev_node(node_list[len(weights_list)])
+- if out_graph.node[next_contig].has_key('path'):
++ if 'path' in out_graph.node[next_contig]:
+ nodeA = rev_node(out_graph.node[next_contig]['path'].split(';')[0])
+ else:
+ nodeA = rev_node(next_contig)
+@@ -419,7 +419,7 @@ with open(outfile, 'w') as f:
+
+ nodeA = rev_node(node_list[0])
+
+- if out_graph.node[prev_contig].has_key('path'):
++ if 'path' in out_graph.node[prev_contig]:
+ nodeB = rev_node(out_graph.node[prev_contig]['path'].split(';')[-1])
+ else:
+ nodeB = rev_node(prev_contig)
+@@ -437,7 +437,7 @@ with open(outfile, 'w') as f:
+
+
+
+-print "Number of contigs: "+str(contig_no)
++print("Number of contigs: "+str(contig_no))
+
+ nx.write_graphml(out_graph,out_graphml_name)
+
+--- a/scripts/get_draft_path_norevcomp.py
++++ b/scripts/get_draft_path_norevcomp.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+ import os
+--- a/scripts/get_single_strand.py
++++ b/scripts/get_single_strand.py
+@@ -1,6 +1,6 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+-#usage python get_single_strand.py <in-fasta> <out-fasta>
++#usage python3 get_single_strand.py <in-fasta> <out-fasta>
+
+ from pbcore.io import FastaIO
+ import sys
+--- a/scripts/interface_utils.py
++++ b/scripts/interface_utils.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+ import os
+@@ -11,40 +11,40 @@ from parse_qv import *
+ #readarg = sys.argv[2]
+
+ def get_reads(filename, readlist):
+- stream = subprocess.Popen(["DBshow", filename] + map(str,readlist),
++ stream = subprocess.Popen(["DBshow", filename] + list(map(str,readlist)),
+ stdout=subprocess.PIPE,bufsize=1)
+ reads = parse_read(stream.stdout) # generator
+ return reads
+
+ def get_QV(filename, readlist):
+- stream = subprocess.Popen(["DBdump", filename, '-i'] + map(str,readlist),
++ stream = subprocess.Popen(["DBdump", filename, '-i'] + list(map(str,readlist)),
+ stdout=subprocess.PIPE,bufsize=1)
+ qv = parse_qv(stream.stdout) # generator
+ return qv
+
+
+ def get_alignments(filename, readlist):
+- stream = subprocess.Popen(["LAshow", filename,filename]+ map(str,readlist),
++ stream = subprocess.Popen(["LAshow", filename,filename]+ list(map(str,readlist)),
+ stdout=subprocess.PIPE,bufsize=1)
+ alignments = parse_alignment(stream.stdout) # generator
+ return alignments
+
+
+ def get_alignments2(filename, alignmentname, readlist):
+- stream = subprocess.Popen(["LA4Awesome", filename, filename, alignmentname]+ map(str,readlist),
++ stream = subprocess.Popen(["LA4Awesome", filename, filename, alignmentname]+ list(map(str,readlist)),
+ stdout=subprocess.PIPE,bufsize=1)
+ alignments = parse_alignment2(stream.stdout) # generator
+ return alignments
+
+
+ def get_alignments_mapping(filename, ref, alignmentname, readlist):
+- stream = subprocess.Popen(["LA4Awesome", filename, ref, alignmentname]+ map(str,readlist)+ ['-F'],
++ stream = subprocess.Popen(["LA4Awesome", filename, ref, alignmentname]+ list(map(str,readlist))+ ['-F'],
+ stdout=subprocess.PIPE,bufsize=1)
+ alignments = parse_alignment2(stream.stdout) # generator
+ return alignments
+
+ def get_alignments_mapping2(ref, filename, alignmentname):
+- print ref,filename,alignmentname
++ print(ref,filename,alignmentname)
+ stream = subprocess.Popen(["LA4Awesome", ref, filename, alignmentname],
+ stdout=subprocess.PIPE,bufsize=1)
+ alignments = parse_alignment2(stream.stdout) # generator
+@@ -53,7 +53,7 @@ def get_alignments_mapping2(ref, filenam
+
+
+ def get_alignments_mapping3(ref, filename, alignmentname, contig_no):
+- print ref,filename,alignmentname
++ print(ref,filename,alignmentname)
+ stream = subprocess.Popen(["LA4Awesome", ref, filename, alignmentname, contig_no],
+ stdout=subprocess.PIPE,bufsize=1)
+ alignments = parse_alignment2(stream.stdout) # generator
+@@ -80,8 +80,8 @@ def get_all_alignments2(filename, alignm
+ def get_all_reads_in_alignment_with_one(filename,read):
+ this_read = get_reads(filename,[read])
+ alignments = list(get_alignments(filename,[read]))
+- readlist = map(lambda x:x[2],alignments)
+- print readlist
++ readlist = [x[2] for x in alignments]
++ print(readlist)
+ other_reads = get_reads(filename,readlist)
+
+ return [list(this_read), list(other_reads), alignments] # note that this is not a generator
+--- a/scripts/longest_path.py
++++ b/scripts/longest_path.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import sys
+@@ -13,7 +13,7 @@ def longest_path(G):
+ dist[node] = max(pairs)
+ else:
+ dist[node] = (0, node)
+- node,(length,_) = max(dist.items(), key=lambda x:x[1])
++ node,(length,_) = max(list(dist.items()), key=lambda x:x[1])
+ path = []
+ while length > 0:
+ path.append(node)
+@@ -27,23 +27,23 @@ filename = sys.argv[1]
+ g = nx.DiGraph()
+
+ with open(filename,'r') as f:
+- for line in f.xreadlines():
++ for line in f:
+ g.add_edge(*(line.strip().split('->')))
+
+
+-print nx.info(g)
+-degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+-print Counter(degree_sequence)
++print(nx.info(g))
++degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++print(Counter(degree_sequence))
+
+ for i in range(7):
+ for node in g.nodes():
+ if g.in_degree(node) == 0:
+ g.remove_node(node)
+
+- print nx.info(g)
++ print(nx.info(g))
+
+-degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+-print Counter(degree_sequence)
++degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++print(Counter(degree_sequence))
+
+
+ def rev(string):
+@@ -57,7 +57,7 @@ for edge in g.edges():
+ #print edge
+ #print rev(edge[1]), rev(edge[0])
+
+-print nx.info(g)
++print(nx.info(g))
+ nx.write_graphml(g, filename.split('.')[0]+'.graphml')
+ #print(list(nx.dfs_edges(g,sys.argv[2])))
+ #p=nx.shortest_path(g)
+--- a/scripts/merge_hinges.py
++++ b/scripts/merge_hinges.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import random
+@@ -70,7 +70,7 @@ def z_clipping(G,threshold,in_hinges,out
+
+ if len(cur_path) <= threshold and H.in_degree(cur_node) > 1 and H.out_degree(st_node) > 1 and cur_node not in in_hinges:
+ if print_z:
+- print cur_path
++ print(cur_path)
+
+ for edge in cur_path:
+ H.remove_edge(edge[0],edge[1])
+@@ -98,7 +98,7 @@ def z_clipping(G,threshold,in_hinges,out
+
+ if len(cur_path) <= threshold and H.out_degree(cur_node) > 1 and H.in_degree(end_node) > 1 and cur_node not in out_hinges:
+ if print_z:
+- print cur_path
++ print(cur_path)
+ for edge in cur_path:
+ H.remove_edge(edge[0],edge[1])
+ for j in range(len(cur_path)-1):
+@@ -167,7 +167,7 @@ def random_condensation(G,n_nodes):
+ merge_path(g,in_node,node,out_node)
+
+ if iter_cnt >= max_iter:
+- print "couldn't finish sparsification"+str(len(g.nodes()))
++ print("couldn't finish sparsification"+str(len(g.nodes())))
+
+ return g
+
+@@ -177,10 +177,10 @@ def add_groundtruth(g,json_file,in_hinge
+
+ mapping = ujson.load(json_file)
+
+- print 'getting mapping'
++ print('getting mapping')
+ mapped_nodes=0
+- print str(len(mapping))
+- print str(len(g.nodes()))
++ print(str(len(mapping)))
++ print(str(len(g.nodes())))
+
+ slack = 500
+
+@@ -191,7 +191,7 @@ def add_groundtruth(g,json_file,in_hinge
+ # print node_base
+
+ #print node
+- if mapping.has_key(node_base):
++ if node_base in mapping:
+ g.node[node]['aln_start'] = min (mapping[node_base][0][0],mapping[node_base][0][1])
+ g.node[node]['aln_end'] = max(mapping[node_base][0][1],mapping[node_base][0][0])
+ # g.node[node]['chr'] = mapping[node_base][0][2]
+@@ -440,7 +440,7 @@ def read_graph(edges_file,hg_file,gt_fil
+
+ hinge_node = lines1[1]+"_"+lines1[4] + '_' + lines1[6]
+
+- print hinge_node
++ print(hinge_node)
+
+ eff_hinge = hinge_mapping[hinge_node]
+
+--- a/scripts/parallel_draw.sh
++++ b/scripts/parallel_draw.sh
+@@ -3,7 +3,7 @@ echo "Bash version ${BASH_VERSION}..."
+ for i in $(seq 4000 1 20000)
+ do
+ echo drawing read $i
+- num1=$(ps -ef | grep 'python draw.py' | wc -l)
++ num1=$(ps -ef | grep 'python3 draw.py' | wc -l)
+ num2=$(ps -ef | grep 'LA4Awesome' | wc -l)
+ num=$(( $num1 + $num2 ))
+ echo $num running
+@@ -11,9 +11,9 @@ for i in $(seq 4000 1 20000)
+ do
+ sleep 5
+ echo waiting, $num running
+- num1=$(ps -ef | grep 'python draw.py' | wc -l)
++ num1=$(ps -ef | grep 'python3 draw.py' | wc -l)
+ num2=$(ps -ef | grep 'LA4Awesome' | wc -l)
+ num=$(( $num1 + $num2 ))
+ done
+- python draw2.py $i &
++ python3 draw2.py $i &
+ done
+--- a/scripts/parallel_draw_large.sh
++++ b/scripts/parallel_draw_large.sh
+@@ -3,7 +3,7 @@ echo "Bash version ${BASH_VERSION}..."
+ for i in $(seq 1 1 100)
+ do
+ echo drawing read $i
+- num1=$(ps -ef | grep 'python draw.py' | wc -l)
++ num1=$(ps -ef | grep 'python3 draw.py' | wc -l)
+ num2=$(ps -ef | grep 'LA4Awesome' | wc -l)
+ num=$(( $num1 + $num2 ))
+ echo $num running
+@@ -12,5 +12,5 @@ for i in $(seq 1 1 100)
+ sleep 5
+ echo waiting
+ done
+- python draw.py $i &
++ python3 draw.py $i &
+ done
+\ No newline at end of file
+--- a/scripts/parse.py
++++ b/scripts/parse.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+ min_len_aln = 1000
+@@ -13,7 +13,7 @@ with sys.stdin as f:
+ read_id = l[0]
+ seq = l[1]
+
+- print read_id,seq
++ print(read_id,seq)
+
+ #if len(seq) > max_len:
+ # seq = seq[:max_len-1]
+--- a/scripts/parse_alignment.py
++++ b/scripts/parse_alignment.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+ import re
+@@ -11,7 +11,7 @@ def parse_alignment(stream = sys.stdin):
+ sub = re.sub(',','',sub)
+ lst = sub.split()[:-1]
+ if len(lst) == 9:
+- yield [lst[2]] + map(int, lst[0:2] + lst[3:])
++ yield [lst[2]] + list(map(int, lst[0:2] + lst[3:]))
+
+
+ def parse_alignment2(stream = sys.stdin):
+@@ -22,5 +22,5 @@ def parse_alignment2(stream = sys.stdin)
+ sub = re.sub(',','',sub)
+ lst = sub.split()[:-1]
+ if len(lst) == 11:
+- yield [lst[2]] + map(int, lst[0:2] + lst[3:])
++ yield [lst[2]] + list(map(int, lst[0:2] + lst[3:]))
+
+--- a/scripts/parse_qv.py
++++ b/scripts/parse_qv.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+
+--- a/scripts/parse_read.py
++++ b/scripts/parse_read.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+
+--- a/scripts/pileup.ipynb
++++ b/scripts/pileup.ipynb
+@@ -205,21 +205,21 @@
+ ],
+ "metadata": {
+ "kernelspec": {
+- "display_name": "Python 2",
+- "language": "python",
+- "name": "python2"
++ "display_name": "Python 3",
++ "language": "python3",
++ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+- "name": "ipython",
+- "version": 2
++ "name": "ipython3",
++ "version": 3
+ },
+ "file_extension": ".py",
+- "mimetype": "text/x-python",
+- "name": "python",
+- "nbconvert_exporter": "python",
+- "pygments_lexer": "ipython2",
+- "version": "2.7.6"
++ "mimetype": "text/x-python3",
++ "name": "python3",
++ "nbconvert_exporter": "python3",
++ "pygments_lexer": "ipython3",
++ "version": "3.7"
+ }
+ },
+ "nbformat": 4,
+--- a/scripts/pipeline_consensus.py
++++ b/scripts/pipeline_consensus.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+ import os
+@@ -38,63 +38,63 @@ base_path = './'
+
+ if st_point <= 1 and end_point >= 1:
+ draft_path_cmd = 'get_draft_path.py '+base_path+' '+ bact_id+' '+graphml_file
+- print '1: '+draft_path_cmd
++ print('1: '+draft_path_cmd)
+ subprocess.check_output(draft_path_cmd,cwd=base_path, shell=True)
+
+
+ if st_point <= 2 and end_point >= 2:
+ draft_assembly_cmd = 'draft_assembly --db '+bact_id+' --las '+bact_id+'.las --prefix '+bact_id+' --config '+ini_path+' --out '+bact_id+'.draft'
+- print '2: '+draft_assembly_cmd
++ print('2: '+draft_assembly_cmd)
+ subprocess.check_output(draft_assembly_cmd,cwd=base_path, shell=True)
+
+
+ if st_point <= 3 and end_point >= 3:
+ corr_head_cmd = 'correct_head.py '+bact_id+'.draft.fasta '+bact_id+'.draft.pb.fasta draft_map.txt'
+- print '3: '+corr_head_cmd
++ print('3: '+corr_head_cmd)
+ subprocess.check_output(corr_head_cmd,cwd=base_path, shell=True)
+
+
+ if st_point <= 4 and end_point >= 4:
+ subprocess.call("rm -f draft.db",shell=True,cwd=base_path)
+ fasta2DB_cmd = "fasta2DB draft "+base_path+bact_id+'.draft.pb.fasta'
+- print '4: '+fasta2DB_cmd
++ print('4: '+fasta2DB_cmd)
+ subprocess.check_output(fasta2DB_cmd.split(),cwd=base_path)
+
+ if st_point <= 5 and end_point >= 5:
+ subprocess.call("rm -f draft.*.las",shell=True,cwd=base_path)
+ mapper_cmd = "HPCmapper draft "+bact_id
+- print '5: '+mapper_cmd
++ print('5: '+mapper_cmd)
+ subprocess.call(mapper_cmd.split(),stdout=open(base_path+'draft_consensus.sh','w') , cwd=base_path)
+
+
+ if st_point <= 6 and end_point >= 6:
+ # modify_cmd = """awk '{gsub("daligner -A -k20 -h50 -e.85","daligner -A",$0); print $0}' draft_consensus.sh"""
+ modify_cmd = ['awk','{gsub("daligner -A -k20 -h50 -e.85","daligner -A",$0); print $0}','draft_consensus.sh']
+- print '6: '+"""awk '{gsub("daligner -A -k20 -h50 -e.85","daligner -A",$0); print $0}' draft_consensus.sh"""
++ print('6: '+"""awk '{gsub("daligner -A -k20 -h50 -e.85","daligner -A",$0); print $0}' draft_consensus.sh""")
+ subprocess.call(modify_cmd,stdout=open(base_path+'draft_consensus2.sh','w') , cwd=base_path)
+
+
+ if st_point <= 7 and end_point >= 7:
+ mapper_shell_cmd = "csh -v draft_consensus.sh"
+- print '7: '+mapper_shell_cmd
++ print('7: '+mapper_shell_cmd)
+ subprocess.check_output(mapper_shell_cmd.split(), cwd=base_path)
+
+ if st_point <= 8 and end_point >= 8:
+ # remove_cmd = 'rm -f nonrevcompdraft.'+bact_id+'.*.las'
+ # subprocess.call(remove_cmd,shell=True,cwd=base_path)
+ LAmerge_cmd = "LAmerge draft."+bact_id+".las "+'draft.'+bact_id+'.[0-9].las'
+- print '8: '+LAmerge_cmd
++ print('8: '+LAmerge_cmd)
+ subprocess.check_output(LAmerge_cmd,cwd=base_path,shell=True)
+
+ if st_point <= 9 and end_point >= 9:
+ consensus_cmd = 'consensus draft '+bact_id+' draft.'+bact_id+'.las '+bact_id+'.consensus.fasta '+ini_path
+- print '9: '+consensus_cmd
++ print('9: '+consensus_cmd)
+ subprocess.check_output(consensus_cmd,cwd=base_path,shell=True)
+
+
+ if st_point <= 10 and end_point >= 10:
+ gfa_cmd = 'get_consensus_gfa.py '+base_path+ ' '+ bact_id+ ' '+bact_id+'.consensus.fasta'
+- print '10: '+gfa_cmd
++ print('10: '+gfa_cmd)
+ subprocess.check_output(gfa_cmd,cwd=base_path,shell=True)
+
+
+--- a/scripts/pipeline_consensus_norevcomp.py
++++ b/scripts/pipeline_consensus_norevcomp.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+
+ import sys
+@@ -39,32 +39,32 @@ base_path = './'
+
+ if st_point <= 1 and end_point >= 1:
+ draft_path_cmd = 'get_draft_path_norevcomp.py '+base_path+' '+ bact_id+' '+graphml_file
+- print '1: '+draft_path_cmd
++ print('1: '+draft_path_cmd)
+ subprocess.check_output(draft_path_cmd,cwd=base_path, shell=True)
+
+
+ if st_point <= 2 and end_point >= 2:
+ draft_assembly_cmd = 'draft_assembly --db '+bact_id+' --las '+bact_id+'.las --prefix '+bact_id+' --config '+ini_path+' --out '+bact_id+'.draft'
+- print '2: '+draft_assembly_cmd
++ print('2: '+draft_assembly_cmd)
+ subprocess.check_output(draft_assembly_cmd,cwd=base_path, shell=True)
+
+
+ if st_point <= 3 and end_point >= 3:
+ corr_head_cmd = 'correct_head.py '+bact_id+'.draft.fasta '+bact_id+'.draft.pb.fasta draft_map.txt'
+- print '3: '+corr_head_cmd
++ print('3: '+corr_head_cmd)
+ subprocess.check_output(corr_head_cmd,cwd=base_path, shell=True)
+
+
+ if st_point <= 4 and end_point >= 4:
+ subprocess.call("rm -f draft.db",shell=True,cwd=base_path)
+ fasta2DB_cmd = "fasta2DB draft "+base_path+bact_id+'.draft.pb.fasta'
+- print '4: '+fasta2DB_cmd
++ print('4: '+fasta2DB_cmd)
+ subprocess.check_output(fasta2DB_cmd.split(),cwd=base_path)
+
+ if st_point <= 5 and end_point >= 5:
+ subprocess.call("rm -f draft.*.las",shell=True,cwd=base_path)
+ mapper_cmd = "HPCmapper draft "+bact_id
+- print '5: '+mapper_cmd
++ print('5: '+mapper_cmd)
+ subprocess.call(mapper_cmd.split(),stdout=open(base_path+'draft_consensus.sh','w') , cwd=base_path)
+
+
+@@ -72,14 +72,14 @@ if st_point <= 5 and end_point >= 5:
+ if st_point <= 6 and end_point >= 6:
+ # modify_cmd = """awk '{gsub("daligner -A -k20 -h50 -e.85","daligner -A",$0); print $0}' draft_consensus.sh"""
+ modify_cmd = ['awk','{gsub("daligner -A -k20 -h50 -e.85","daligner -A",$0); print $0}','draft_consensus.sh']
+- print '6: '+"""awk '{gsub("daligner -A -k20 -h50 -e.85","daligner -A",$0); print $0}' draft_consensus.sh"""
++ print('6: '+"""awk '{gsub("daligner -A -k20 -h50 -e.85","daligner -A",$0); print $0}' draft_consensus.sh""")
+ subprocess.call(modify_cmd,stdout=open(base_path+'draft_consensus2.sh','w') , cwd=base_path)
+
+
+
+ if st_point <= 7 and end_point >= 7:
+ mapper_shell_cmd = "csh -v draft_consensus2.sh"
+- print '7: '+mapper_shell_cmd
++ print('7: '+mapper_shell_cmd)
+ subprocess.check_output(mapper_shell_cmd.split(), cwd=base_path)
+
+
+@@ -87,13 +87,13 @@ if st_point <= 8 and end_point >= 8:
+ # remove_cmd = 'rm -f nonrevcompdraft.'+bact_id+'.*.las'
+ # subprocess.call(remove_cmd,shell=True,cwd=base_path)
+ LAmerge_cmd = "LAmerge draft."+bact_id+".las "+'draft.'+bact_id+'.[0-9].las'
+- print '8: '+LAmerge_cmd
++ print('8: '+LAmerge_cmd)
+ subprocess.check_output(LAmerge_cmd,cwd=base_path,shell=True)
+
+
+ if st_point <= 9 and end_point >= 9:
+ consensus_cmd = 'consensus draft '+bact_id+' draft.'+bact_id+'.las '+bact_id+'.norevcomp_consensus.fasta '+ini_path
+- print '9: '+consensus_cmd
++ print('9: '+consensus_cmd)
+ subprocess.check_output(consensus_cmd,cwd=base_path,shell=True)
+
+
+--- a/scripts/pipeline_nctc.py
++++ b/scripts/pipeline_nctc.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+ import os
+@@ -27,35 +27,35 @@ assert len(fasta_names)==1
+ fasta_name = fasta_names[0]
+ bact_name = fasta_name.split('.fasta')[0]
+
+-print bact_name
++print(bact_name)
+
+
+ if st_point <= 1:
+ subprocess.call("rm -f *.db",shell=True,cwd=base_path)
+ fasta2DB_cmd = "fasta2DB "+bact_name+' '+base_path+fasta_name
+- print fasta2DB_cmd
++ print(fasta2DB_cmd)
+ subprocess.check_output(fasta2DB_cmd.split(),cwd=base_path)
+
+ if st_point <= 2:
+ DBsplit_cmd = "DBsplit -x500 -s100 "+bact_name
+- print DBsplit_cmd
++ print(DBsplit_cmd)
+ subprocess.check_output(DBsplit_cmd.split(),cwd=base_path)
+
+ if st_point <= 3:
+ subprocess.call("rm -f *.las",shell=True,cwd=base_path)
+ daligner_cmd = "HPCdaligner -t5 "+bact_name
+ daligner_shell_cmd = "csh -v daligner_cmd.sh"
+- print daligner_cmd
++ print(daligner_cmd)
+ p = subprocess.call(daligner_cmd.split(),stdout=open(base_path+'daligner_cmd.sh','w') , cwd=base_path)
+ p2 = subprocess.check_output(daligner_shell_cmd.split(), cwd=base_path)
+ if st_point <= 4:
+ remove_cmd = "rm "+base_path+bact_name+".*."+bact_name+".*"
+- print remove_cmd
++ print(remove_cmd)
+ os.system(remove_cmd)
+
+ if st_point <= 5:
+ LAmerge_cmd = "LAmerge "+bact_name+".las "+bact_name+".*.las"
+- print LAmerge_cmd
++ print(LAmerge_cmd)
+ subprocess.check_output(LAmerge_cmd,cwd=base_path,shell=True)
+
+ if st_point <= 6:
+@@ -71,17 +71,17 @@ if st_point <= 8:
+
+ if st_point <= 9:
+ Reads_filter_cmd = "Reads_filter --db "+bact_name+" --las "+bact_name+".las -x "+bact_name+" --config ~/AwesomeAssembler/utils/nominal.ini"
+- print Reads_filter_cmd
++ print(Reads_filter_cmd)
+ subprocess.check_output(Reads_filter_cmd,cwd=base_path, shell=True)
+
+ if st_point <= 10:
+ hinging_cmd = "hinging --db "+bact_name+" --las "+bact_name+".las -x "+bact_name+" --config ~/AwesomeAssembler/utils/nominal.ini -o "+bact_name
+- print hinging_cmd
++ print(hinging_cmd)
+ subprocess.check_output(hinging_cmd, cwd=base_path, shell=True)
+
+ if st_point <= 11:
+- pruning_cmd = "python ~/AwesomeAssembler/scripts/pruning_and_clipping.py "+bact_name+".edges.hinges "+bact_name+".hinge.list A"
+- print pruning_cmd
++ pruning_cmd = "python3 /usr/lib/hinge/pruning_and_clipping.py "+bact_name+".edges.hinges "+bact_name+".hinge.list A"
++ print(pruning_cmd)
+ subprocess.check_output(pruning_cmd, cwd=base_path, shell=True)
+
+
+--- a/scripts/pruning_and_clipping.py
++++ b/scripts/pruning_and_clipping.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ # coding: utf-8
+
+@@ -39,7 +39,7 @@ def write_graph2(G,Ginfo,flname):
+
+ if (edge[0],edge[1]) not in Ginfo:
+ count_no += 1
+- print "not found"
++ print("not found")
+ continue
+ else:
+ count_yes += 1
+@@ -54,7 +54,7 @@ def write_graph2(G,Ginfo,flname):
+
+ f.write(Ginfo[(edge[0],edge[1])]+'\n')
+
+- print count_no, count_yes
++ print(count_no, count_yes)
+
+
+
+@@ -90,7 +90,7 @@ def prune_graph(graph,in_hinges,out_hing
+ H.add_node(successor)
+ for node in in_hinges:
+ H.add_node(node)
+- map(H.add_node,start_nodes)
++ list(map(H.add_node,start_nodes))
+ all_vertices=set(G.nodes())
+ current_vertices=set(H.nodes())
+ undiscovered_vertices=all_vertices-current_vertices
+@@ -107,10 +107,10 @@ def prune_graph(graph,in_hinges,out_hing
+ current_vertices=current_vertices.union(discovered_vertices_set)
+ # print len(undiscovered_vertices)
+ if len(discovered_vertices_set)==0:
+- print last_discovered_vertices
+- print 'did not reach all nodes'
+- print 'size of G: '+str(len(G.nodes()))
+- print 'size of H: '+str(len(H.nodes()))
++ print(last_discovered_vertices)
++ print('did not reach all nodes')
++ print('size of G: '+str(len(G.nodes())))
++ print('size of H: '+str(len(H.nodes())))
+ # return H
+
+ rand_node = list(undiscovered_vertices)[0]
+@@ -206,20 +206,20 @@ def dead_end_clipping_sym(G,threshold,pr
+
+ cur_node = st_node
+ if print_debug:
+- print '----0'
+- print st_node
++ print('----0')
++ print(st_node)
+
+ if len(H.successors(st_node)) == 1:
+ cur_node = H.successors(st_node)[0]
+
+ if print_debug:
+- print '----1'
++ print('----1')
+
+ while H.in_degree(cur_node) == 1 and H.out_degree(cur_node) == 1 and len(cur_path) < threshold + 2:
+ cur_path.append(cur_node)
+
+ if print_debug:
+- print cur_node
++ print(cur_node)
+
+ cur_node = H.successors(cur_node)[0]
+
+@@ -228,21 +228,21 @@ def dead_end_clipping_sym(G,threshold,pr
+
+
+ if print_debug:
+- print '----2'
+- print cur_path
++ print('----2')
++ print(cur_path)
+
+
+ if len(cur_path) <= threshold and (H.in_degree(cur_node) > 1 or H.out_degree(cur_node) == 0):
+ for vertex in cur_path:
+ # try:
+ if print_debug:
+- print 'about to delete ',vertex,rev_node(vertex)
++ print('about to delete ',vertex,rev_node(vertex))
+ H.remove_node(vertex)
+ H.remove_node(rev_node(vertex))
+ # except:
+ # pass
+ if print_debug:
+- print 'deleted ',vertex,rev_node(vertex)
++ print('deleted ',vertex,rev_node(vertex))
+
+
+ return H
+@@ -276,7 +276,7 @@ def z_clipping(G,threshold,in_hinges,out
+
+ if len(cur_path) <= threshold and H.in_degree(cur_node) > 1 and H.out_degree(st_node) > 1 and cur_node not in in_hinges:
+ if print_z:
+- print cur_path
++ print(cur_path)
+
+ for edge in cur_path:
+ H.remove_edge(edge[0],edge[1])
+@@ -304,7 +304,7 @@ def z_clipping(G,threshold,in_hinges,out
+
+ if len(cur_path) <= threshold and H.out_degree(cur_node) > 1 and H.in_degree(end_node) > 1 and cur_node not in out_hinges:
+ if print_z:
+- print cur_path
++ print(cur_path)
+ for edge in cur_path:
+ H.remove_edge(edge[0],edge[1])
+ for j in range(len(cur_path)-1):
+@@ -346,7 +346,7 @@ def z_clipping_sym(G,threshold,in_hinges
+
+ if len(cur_path) <= threshold and H.in_degree(cur_node) > 1 and H.out_degree(st_node) > 1 and cur_node not in in_hinges:
+ if print_z:
+- print cur_path
++ print(cur_path)
+
+ for edge in cur_path:
+
+@@ -432,7 +432,7 @@ def random_condensation(G,n_nodes,check_
+ merge_path(g,in_node,node,out_node)
+
+ if iter_cnt >= max_iter:
+- print "couldn't finish sparsification"+str(len(g.nodes()))
++ print("couldn't finish sparsification"+str(len(g.nodes())))
+
+ return g
+
+@@ -478,7 +478,7 @@ def random_condensation_sym(G,n_nodes,ch
+ pass
+
+ if iter_cnt >= max_iter:
+- print "couldn't finish sparsification"+str(len(g.nodes()))
++ print("couldn't finish sparsification"+str(len(g.nodes())))
+
+ return g
+
+@@ -535,7 +535,7 @@ def random_condensation2(g,n_nodes):
+
+
+ if iter_cnt >= max_iter:
+- print "couldn't finish sparsification: "+str(len(g.nodes()))
++ print("couldn't finish sparsification: "+str(len(g.nodes())))
+
+
+ return g
+@@ -583,7 +583,7 @@ def bubble_bursting_sym(H,threshold,prin
+ if len(cur_path) <= threshold and len(alt_path) <= threshold and end_node0 == cur_node:
+
+ if print_bubble:
+- print 'found bubble'
++ print('found bubble')
+
+ for edge in cur_path:
+
+@@ -692,8 +692,8 @@ def loop_resolution(g,max_nodes,flank,pr
+ starting_nodes = [x for x in g.nodes() if g.out_degree(x) == 2]
+
+ if print_debug:
+- print '----'
+- print starting_nodes
++ print('----')
++ print(starting_nodes)
+
+ tandem = []
+
+@@ -704,8 +704,8 @@ def loop_resolution(g,max_nodes,flank,pr
+ continue
+
+ if print_debug:
+- print '----'
+- print st_node
++ print('----')
++ print(st_node)
+
+ loop_len = 0
+
+@@ -716,14 +716,14 @@ def loop_resolution(g,max_nodes,flank,pr
+ continue
+
+ if print_debug:
+- print '----'
+- print first_node
++ print('----')
++ print(first_node)
+
+ other_successor = [x for x in g.successors(st_node) if x != first_node][0]
+
+ next_node = first_node
+ if print_debug:
+- print 'going on loop'
++ print('going on loop')
+
+ loop_len = 0
+ prev_edge = g[st_node][next_node]
+@@ -739,7 +739,7 @@ def loop_resolution(g,max_nodes,flank,pr
+ continue
+
+ if print_debug:
+- print "length in loop " + str(loop_len)
++ print("length in loop " + str(loop_len))
+ len_in_loop = loop_len
+ first_node_of_repeat = next_node
+
+@@ -780,8 +780,8 @@ def loop_resolution(g,max_nodes,flank,pr
+ try:
+ assert not (g.in_degree(next_double_node) == 1 and g.out_degree(next_double_node) == 1)
+ except:
+- print str(g.in_degree(next_node))
+- print str(g.out_degree(next_node))
++ print(str(g.in_degree(next_node)))
++ print(str(g.out_degree(next_node)))
+ raise
+
+ while g.in_degree(next_double_node) == 1 and g.out_degree(next_double_node) == 1 and node_cnt < max_nodes:
+@@ -791,16 +791,16 @@ def loop_resolution(g,max_nodes,flank,pr
+ rep.append(next_double_node)
+
+ if print_debug:
+- print "length in repeat " + str(loop_len-len_in_loop)
++ print("length in repeat " + str(loop_len-len_in_loop))
+
+ if next_double_node == st_node and loop_len > MAX_PLASMID_LENGTH:
+ if print_debug:
+- print 'success!'
+- print "length in loop " + str(loop_len)
+- print 'rep is:'
+- print rep
+- print 'in_node and other_successor:'
+- print in_node, other_successor
++ print('success!')
++ print("length in loop " + str(loop_len))
++ print('rep is:')
++ print(rep)
++ print('in_node and other_successor:')
++ print(in_node, other_successor)
+ resolve_rep(g,rep,in_node,other_successor)
+ # print next_double_node
+
+@@ -880,10 +880,10 @@ def add_groundtruth(g,json_file,in_hinge
+
+ mapping = ujson.load(json_file)
+
+- print 'getting mapping'
++ print('getting mapping')
+ mapped_nodes=0
+- print str(len(mapping))
+- print str(len(g.nodes()))
++ print(str(len(mapping)))
++ print(str(len(g.nodes())))
+
+ slack = 500
+ max_chr = 0
+@@ -897,7 +897,7 @@ def add_groundtruth(g,json_file,in_hinge
+
+ #print node
+ g.node[node]['normpos'] = 0
+- if mapping.has_key(node_base):
++ if node_base in mapping:
+ g.node[node]['chr'] = mapping[node_base][0][2]+1
+ g.node[node]['aln_start'] = min (mapping[node_base][0][0],mapping[node_base][0][1])
+ g.node[node]['aln_end'] = max(mapping[node_base][0][1],mapping[node_base][0][0])
+@@ -922,22 +922,22 @@ def add_groundtruth(g,json_file,in_hinge
+ else:
+ chr_length_dict[g.node[node]['chr']] = max(g.node[node]['aln_end'], 1)
+
+- chr_list = sorted(chr_length_dict.items(), key=operator.itemgetter(1), reverse=True)
++ chr_list = sorted(list(chr_length_dict.items()), key=operator.itemgetter(1), reverse=True)
+
+ max_chr_len1 = max([g.node[x]['aln_end'] for x in g.nodes()])
+ max_chr_multiplier = 10**len(str(max_chr_len1))
+- print [x for x in chr_list]
++ print([x for x in chr_list])
+ chr_set =[x [0] for x in chr_list]
+- print chr_set
++ print(chr_set)
+ # red_bk = 102
+ # green_bk = 102
+ # blue_bk = 102
+ colour_list = ['red', 'lawngreen', 'deepskyblue', 'deeppink', 'darkorange', 'purple', 'gold', 'mediumblue', 'saddlebrown', 'darkgreen']
+ for colour in colour_list:
+- print matplotlib.colors.colorConverter.to_rgb(colour)
++ print(matplotlib.colors.colorConverter.to_rgb(colour))
+ for index, chrom in enumerate(chr_set):
+ node_set = set([x for x in g.nodes() if g.node[x]['chr'] == chrom])
+- print chrom
++ print(chrom)
+
+
+ max_chr_len = max([g.node[x]['aln_end'] for x in g.nodes() if g.node[x]['chr'] == chrom])
+@@ -960,7 +960,7 @@ def add_groundtruth(g,json_file,in_hinge
+ blue_bk = max(blue-100,0)
+ green_bk = max(green-100,0)
+
+- print red,blue,green
++ print(red,blue,green)
+ for node in node_set:
+ g.node[node]['normpos'] = g.node[node]['chr'] * max_chr_multiplier + (g.node[node]['aln_end']/float(max_chr_len))*max_chr_multiplier
+ lamda = (g.node[node]['aln_end']/max_chr_len)
+@@ -1058,13 +1058,13 @@ def add_chimera_flags(g,prefix):
+ assert not ((node_name+'_0' in node_set and node_name+'_1' not in node_set)
+ or (node_name+'_0' not in node_set and node_name+'_1' in node_set))
+ except:
+- print node_name + ' is not symmetrically present in the graph input.'
++ print(node_name + ' is not symmetrically present in the graph input.')
+ raise
+ if node_name+'_0' in node_set:
+ g.node[node_name+'_0']['CFLAG'] = True
+ g.node[node_name+'_1']['CFLAG'] = True
+ num_bad_cov_reads += 1
+- print str(num_bad_cov_reads) + ' bad coverage reads.'
++ print(str(num_bad_cov_reads) + ' bad coverage reads.')
+
+ num_bad_slf_reads = 0
+ if slf_flags != None:
+@@ -1075,13 +1075,13 @@ def add_chimera_flags(g,prefix):
+ assert not ((node_name+'_0' in node_set and node_name+'_1' not in node_set)
+ or (node_name+'_0' not in node_set and node_name+'_1' in node_set))
+ except:
+- print node_name + ' is not symmetrically present in the graph input.'
++ print(node_name + ' is not symmetrically present in the graph input.')
+ raise
+ if node_name+'_0' in node_set:
+ g.node[node_name+'_0']['SFLAG'] = True
+ g.node[node_name+'_1']['SFLAG'] = True
+ num_bad_slf_reads += 1
+- print str(num_bad_slf_reads) + ' bad self aligned reads.'
++ print(str(num_bad_slf_reads) + ' bad self aligned reads.')
+
+
+
+--- a/scripts/pruning_and_clipping_nanopore.py
++++ b/scripts/pruning_and_clipping_nanopore.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ # coding: utf-8
+
+@@ -36,7 +36,7 @@ def write_graph2(G,Ginfo,flname):
+
+ if (edge[0],edge[1]) not in Ginfo:
+ count_no += 1
+- print "not found"
++ print("not found")
+ continue
+ else:
+ count_yes += 1
+@@ -51,7 +51,7 @@ def write_graph2(G,Ginfo,flname):
+
+ f.write(Ginfo[(edge[0],edge[1])]+'\n')
+
+- print count_no, count_yes
++ print(count_no, count_yes)
+
+
+
+@@ -87,7 +87,7 @@ def prune_graph(graph,in_hinges,out_hing
+ H.add_node(successor)
+ for node in in_hinges:
+ H.add_node(node)
+- map(H.add_node,start_nodes)
++ list(map(H.add_node,start_nodes))
+ all_vertices=set(G.nodes())
+ current_vertices=set(H.nodes())
+ undiscovered_vertices=all_vertices-current_vertices
+@@ -104,10 +104,10 @@ def prune_graph(graph,in_hinges,out_hing
+ current_vertices=current_vertices.union(discovered_vertices_set)
+ # print len(undiscovered_vertices)
+ if len(discovered_vertices_set)==0:
+- print last_discovered_vertices
+- print 'did not reach all nodes'
+- print 'size of G: '+str(len(G.nodes()))
+- print 'size of H: '+str(len(H.nodes()))
++ print(last_discovered_vertices)
++ print('did not reach all nodes')
++ print('size of G: '+str(len(G.nodes())))
++ print('size of H: '+str(len(H.nodes())))
+ # return H
+
+ rand_node = list(undiscovered_vertices)[0]
+@@ -203,20 +203,20 @@ def dead_end_clipping_sym(G,threshold,pr
+
+ cur_node = st_node
+ if print_debug:
+- print '----0'
+- print st_node
++ print('----0')
++ print(st_node)
+
+ if len(H.successors(st_node)) == 1:
+ cur_node = H.successors(st_node)[0]
+
+ if print_debug:
+- print '----1'
++ print('----1')
+
+ while H.in_degree(cur_node) == 1 and H.out_degree(cur_node) == 1 and len(cur_path) < threshold + 2:
+ cur_path.append(cur_node)
+
+ if print_debug:
+- print cur_node
++ print(cur_node)
+
+ cur_node = H.successors(cur_node)[0]
+
+@@ -225,21 +225,21 @@ def dead_end_clipping_sym(G,threshold,pr
+
+
+ if print_debug:
+- print '----2'
+- print cur_path
++ print('----2')
++ print(cur_path)
+
+
+ if len(cur_path) <= threshold and (H.in_degree(cur_node) > 1 or H.out_degree(cur_node) == 0):
+ for vertex in cur_path:
+ # try:
+ if print_debug:
+- print 'about to delete ',vertex,rev_node(vertex)
++ print('about to delete ',vertex,rev_node(vertex))
+ H.remove_node(vertex)
+ H.remove_node(rev_node(vertex))
+ # except:
+ # pass
+ if print_debug:
+- print 'deleted ',vertex,rev_node(vertex)
++ print('deleted ',vertex,rev_node(vertex))
+
+
+ return H
+@@ -273,7 +273,7 @@ def z_clipping(G,threshold,in_hinges,out
+
+ if len(cur_path) <= threshold and H.in_degree(cur_node) > 1 and H.out_degree(st_node) > 1 and cur_node not in in_hinges:
+ if print_z:
+- print cur_path
++ print(cur_path)
+
+ for edge in cur_path:
+ H.remove_edge(edge[0],edge[1])
+@@ -301,7 +301,7 @@ def z_clipping(G,threshold,in_hinges,out
+
+ if len(cur_path) <= threshold and H.out_degree(cur_node) > 1 and H.in_degree(end_node) > 1 and cur_node not in out_hinges:
+ if print_z:
+- print cur_path
++ print(cur_path)
+ for edge in cur_path:
+ H.remove_edge(edge[0],edge[1])
+ for j in range(len(cur_path)-1):
+@@ -343,7 +343,7 @@ def z_clipping_sym(G,threshold,in_hinges
+
+ if len(cur_path) <= threshold and H.in_degree(cur_node) > 1 and H.out_degree(st_node) > 1 and cur_node not in in_hinges:
+ if print_z:
+- print cur_path
++ print(cur_path)
+
+ for edge in cur_path:
+
+@@ -429,7 +429,7 @@ def random_condensation(G,n_nodes,check_
+ merge_path(g,in_node,node,out_node)
+
+ if iter_cnt >= max_iter:
+- print "couldn't finish sparsification"+str(len(g.nodes()))
++ print("couldn't finish sparsification"+str(len(g.nodes())))
+
+ return g
+
+@@ -475,7 +475,7 @@ def random_condensation_sym(G,n_nodes,ch
+ pass
+
+ if iter_cnt >= max_iter:
+- print "couldn't finish sparsification"+str(len(g.nodes()))
++ print("couldn't finish sparsification"+str(len(g.nodes())))
+
+ return g
+
+@@ -532,7 +532,7 @@ def random_condensation2(g,n_nodes):
+
+
+ if iter_cnt >= max_iter:
+- print "couldn't finish sparsification: "+str(len(g.nodes()))
++ print("couldn't finish sparsification: "+str(len(g.nodes())))
+
+
+ return g
+@@ -580,7 +580,7 @@ def bubble_bursting_sym(H,threshold,prin
+ if len(cur_path) <= threshold and len(alt_path) <= threshold and end_node0 == cur_node:
+
+ if print_bubble:
+- print 'found bubble'
++ print('found bubble')
+
+ for edge in cur_path:
+
+@@ -689,8 +689,8 @@ def loop_resolution(g,max_nodes,flank,pr
+ starting_nodes = [x for x in g.nodes() if g.out_degree(x) == 2]
+
+ if print_debug:
+- print '----'
+- print starting_nodes
++ print('----')
++ print(starting_nodes)
+
+ tandem = []
+
+@@ -701,8 +701,8 @@ def loop_resolution(g,max_nodes,flank,pr
+ continue
+
+ if print_debug:
+- print '----'
+- print st_node
++ print('----')
++ print(st_node)
+
+
+ for first_node in g.successors(st_node):
+@@ -712,14 +712,14 @@ def loop_resolution(g,max_nodes,flank,pr
+ continue
+
+ if print_debug:
+- print '----'
+- print first_node
++ print('----')
++ print(first_node)
+
+ other_successor = [x for x in g.successors(st_node) if x != first_node][0]
+
+ next_node = first_node
+ if print_debug:
+- print 'going on loop'
++ print('going on loop')
+
+ node_cnt = 0
+ while g.in_degree(next_node) == 1 and g.out_degree(next_node) == 1 and node_cnt < max_nodes:
+@@ -771,11 +771,11 @@ def loop_resolution(g,max_nodes,flank,pr
+
+ if next_double_node == st_node:
+ if print_debug:
+- print 'success!'
+- print 'rep is:'
+- print rep
+- print 'in_node and other_successor:'
+- print in_node, other_successor
++ print('success!')
++ print('rep is:')
++ print(rep)
++ print('in_node and other_successor:')
++ print(in_node, other_successor)
+ resolve_rep(g,rep,in_node,other_successor)
+ # print next_double_node
+
+@@ -805,10 +805,10 @@ def add_groundtruth(g,json_file,in_hinge
+
+ mapping = ujson.load(json_file)
+
+- print 'getting mapping'
++ print('getting mapping')
+ mapped_nodes=0
+- print str(len(mapping))
+- print str(len(g.nodes()))
++ print(str(len(mapping)))
++ print(str(len(g.nodes())))
+
+ slack = 500
+ max_chr = 0
+@@ -822,7 +822,7 @@ def add_groundtruth(g,json_file,in_hinge
+
+ #print node
+ g.node[node]['normpos'] = 0
+- if mapping.has_key(node_base):
++ if node_base in mapping:
+ g.node[node]['chr'] = mapping[node_base][0][2]+1
+ g.node[node]['aln_start'] = min (mapping[node_base][0][0],mapping[node_base][0][1])
+ g.node[node]['aln_end'] = max(mapping[node_base][0][1],mapping[node_base][0][0])
+@@ -847,22 +847,22 @@ def add_groundtruth(g,json_file,in_hinge
+ else:
+ chr_length_dict[g.node[node]['chr']] = max(g.node[node]['aln_end'], 1)
+
+- chr_list = sorted(chr_length_dict.items(), key=operator.itemgetter(1), reverse=True)
++ chr_list = sorted(list(chr_length_dict.items()), key=operator.itemgetter(1), reverse=True)
+
+ max_chr_len1 = max([g.node[x]['aln_end'] for x in g.nodes()])
+ max_chr_multiplier = 10**len(str(max_chr_len1))
+- print [x for x in chr_list]
++ print([x for x in chr_list])
+ chr_set =[x [0] for x in chr_list]
+- print chr_set
++ print(chr_set)
+ # red_bk = 102
+ # green_bk = 102
+ # blue_bk = 102
+ colour_list = ['red', 'lawngreen', 'deepskyblue', 'deeppink', 'darkorange', 'purple', 'gold', 'mediumblue', 'saddlebrown', 'darkgreen']
+ for colour in colour_list:
+- print matplotlib.colors.colorConverter.to_rgb(colour)
++ print(matplotlib.colors.colorConverter.to_rgb(colour))
+ for index, chrom in enumerate(chr_set):
+ node_set = set([x for x in g.nodes() if g.node[x]['chr'] == chrom])
+- print chrom
++ print(chrom)
+
+
+ max_chr_len = max([g.node[x]['aln_end'] for x in g.nodes() if g.node[x]['chr'] == chrom])
+@@ -885,7 +885,7 @@ def add_groundtruth(g,json_file,in_hinge
+ blue_bk = max(blue-100,0)
+ green_bk = max(green-100,0)
+
+- print red,blue,green
++ print(red,blue,green)
+ for node in node_set:
+ g.node[node]['normpos'] = g.node[node]['chr'] * max_chr_multiplier + (g.node[node]['aln_end']/float(max_chr_len))*max_chr_multiplier
+ lamda = (g.node[node]['aln_end']/max_chr_len)
+--- a/scripts/random_condensation.py
++++ b/scripts/random_condensation.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import networkx as nx
+ import random
+@@ -9,7 +9,7 @@ from collections import Counter
+
+ # This script does a random condensation of the graph down to 2000 nodes
+
+-# python random_condensation.py ecoli.edges 2000
++# python3 random_condensation.py ecoli.edges 2000
+
+ # It also keeps the ground truth on the graph through the condensation steps (if a json file is available)
+
+@@ -23,7 +23,7 @@ def merge_path(g,in_node,node,out_node):
+
+ def input1(flname):
+
+- print "input1"
++ print("input1")
+
+ g = nx.DiGraph()
+ with open (flname) as f:
+@@ -39,7 +39,7 @@ def input1(flname):
+
+ def input2(flname):
+
+- print "input2"
++ print("input2")
+
+ g = nx.DiGraph()
+ with open (flname) as f:
+@@ -53,7 +53,7 @@ def input2(flname):
+
+ def input3(flname):
+
+- print "input3"
++ print("input3")
+ # g = nx.DiGraph()
+ g = nx.read_graphml(flname)
+
+@@ -65,7 +65,7 @@ def de_clip(filename, n_nodes, hinge_lis
+
+ f=open(filename)
+ line1=f.readline()
+- print line1
++ print(line1)
+ f.close()
+
+ extension = filename.split('.')[-1]
+@@ -78,28 +78,28 @@ def de_clip(filename, n_nodes, hinge_lis
+ g=input2(filename)
+
+
+- print nx.info(g)
+- degree_sequence=sorted(g.degree().values(),reverse=True)
+- print Counter(degree_sequence)
++ print(nx.info(g))
++ degree_sequence=sorted(list(g.degree().values()),reverse=True)
++ print(Counter(degree_sequence))
+
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+ try:
+ import ujson
+ mapping = ujson.load(open(gt_file))
+
+- print 'getting mapping'
++ print('getting mapping')
+ mapped_nodes=0
+- print str(len(mapping))
+- print str(len(g.nodes()))
++ print(str(len(mapping)))
++ print(str(len(g.nodes())))
+ for node in g.nodes():
+ # print node
+ node_base=node.split("_")[0]
+ # print node_base
+
+ #print node
+- if mapping.has_key(node_base):
++ if node_base in mapping:
+ g.node[node]['aln_start'] = min (mapping[node_base][0][0],mapping[node_base][0][1])
+ g.node[node]['aln_end'] = max(mapping[node_base][0][1],mapping[node_base][0][0])
+ g.node[node]['chr'] = mapping[node_base][0][2]
+@@ -127,9 +127,9 @@ def de_clip(filename, n_nodes, hinge_lis
+ raise
+ # print "json "+filename.split('.')[0]+'.mapping.json'+" not found. exiting."
+
+- print hinge_list
++ print(hinge_list)
+
+- print str(mapped_nodes)+" out of " +str(len(g.nodes()))+" nodes mapped."
++ print(str(mapped_nodes)+" out of " +str(len(g.nodes()))+" nodes mapped.")
+
+ # for i in range(5):
+ # merge_simple_path(g)
+@@ -141,7 +141,7 @@ def de_clip(filename, n_nodes, hinge_lis
+ num_iter=10000
+ iter_done=0
+ if hinge_list != None:
+- print "Found hinge list."
++ print("Found hinge list.")
+ with open(hinge_list,'r') as f:
+ for lines in f:
+ lines1=lines.split()
+@@ -153,7 +153,7 @@ def de_clip(filename, n_nodes, hinge_lis
+ in_hinges.add(lines1[0]+'_1')
+ out_hinges.add(lines1[0]+'_0')
+
+- print str(len(in_hinges))+' hinges found.'
++ print(str(len(in_hinges))+' hinges found.')
+
+ for node in g.nodes():
+ if node in in_hinges and node in out_hinges:
+@@ -205,7 +205,7 @@ def de_clip(filename, n_nodes, hinge_lis
+
+ for nd in g.nodes():
+ if len(nd.split("_"))==1:
+- print nd + " in trouble"
++ print(nd + " in trouble")
+ # in_node = g.in_edges(node2)[0][0]
+ # out_node = g.out_edges(node2)[0][1]
+ # if g.node[node2]['hinge']==0 and g.node[in_node]['hinge']==0 and g.node[out_node]['hinge']==0:
+@@ -260,24 +260,24 @@ def de_clip(filename, n_nodes, hinge_lis
+
+
+
+- degree_sequence=sorted(nx.degree(g).values(),reverse=True)
+- print Counter(degree_sequence)
++ degree_sequence=sorted(list(nx.degree(g).values()),reverse=True)
++ print(Counter(degree_sequence))
+
+
+ nx.write_graphml(g, filename.split('.')[0]+'.sparse3.graphml')
+
+- print nx.number_weakly_connected_components(g)
+- print nx.number_strongly_connected_components(g)
++ print(nx.number_weakly_connected_components(g))
++ print(nx.number_strongly_connected_components(g))
+
+
+ if __name__ == "__main__":
+ filename = sys.argv[1]
+ try :
+ hinge_list=sys.argv[3]
+- print "Found hinge list."
++ print("Found hinge list.")
+ except:
+ hinge_list=None
+- print "in except "+hinge_list
++ print("in except "+hinge_list)
+
+ de_clip(filename, int(sys.argv[2]),hinge_list, sys.argv[4])
+
+--- a/scripts/repeat_annotate_reads.py
++++ b/scripts/repeat_annotate_reads.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+ import os
+--- a/scripts/run_mapping.py
++++ b/scripts/run_mapping.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import sys
+ import os
+ import subprocess
+@@ -17,7 +17,7 @@ alignments = parse_alignment2(stream.std
+
+ d = {}
+ for alignment in alignments:
+- if not d.has_key(alignment[2]):
++ if alignment[2] not in d:
+ d[alignment[2]] = []
+ d[alignment[2]].append([alignment[0],alignment[3],alignment[4], alignment[6], alignment[7], alignment[1]])
+
+@@ -25,7 +25,7 @@ for alignment in alignments:
+
+ mapping = {}
+
+-for key,value in d.items():
++for key,value in list(d.items()):
+ value.sort(key = lambda x:x[2]-x[1], reverse=True)
+ aln = value[0]
+
+--- a/scripts/run_mapping2.py
++++ b/scripts/run_mapping2.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import sys
+ import os
+ import subprocess
+@@ -18,7 +18,7 @@ alignments = parse_alignment2(stream.std
+
+ d = {}
+ for alignment in alignments:
+- if not d.has_key(alignment[2]):
++ if alignment[2] not in d:
+ d[alignment[2]] = []
+ d[alignment[2]].append([alignment[0],alignment[3],alignment[4], alignment[6], alignment[7], alignment[1]])
+
+@@ -26,13 +26,13 @@ for alignment in alignments:
+
+ mapping = {}
+
+-for key,value in d.items():
++for key,value in list(d.items()):
+ value.sort(key = lambda x:x[2]-x[1], reverse=True)
+ alns = value[:k]
+ max_val=alns[0][2]-alns[0][1]
+ for aln in alns:
+ if aln[2]-aln[1] > max_val/2.:
+- if not mapping.has_key(str(key)):
++ if str(key) not in mapping:
+ mapping[str(key)] = [(aln[1], aln[2],aln[-1], 1-int(aln[0] == 'n'))]
+ # mapping[str(key)+'\''] = [(aln[2], aln[1],aln[-1], int(aln[0] == 'n'))]
+ else:
+--- a/scripts/run_mapping3.py
++++ b/scripts/run_mapping3.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import sys
+ import os
+ import subprocess
+@@ -18,7 +18,7 @@ alignments = parse_alignment2(stream.std
+
+ d = {}
+ for alignment in alignments:
+- if not d.has_key(alignment[2]):
++ if alignment[2] not in d:
+ d[alignment[2]] = []
+ d[alignment[2]].append([alignment[0],alignment[3],alignment[4], alignment[6], alignment[7], alignment[1]])
+
+@@ -26,13 +26,13 @@ for alignment in alignments:
+
+ mapping = {}
+
+-for key,value in d.items():
++for key,value in list(d.items()):
+ value.sort(key = lambda x:x[2]-x[1], reverse=True)
+ #alns = value[:k]
+ if len(alns) > 0:
+ alns = [item for item in alns if (item[2] - item[1]) > (alns[0][2] - alns[0][1])/2]
+ for aln in alns:
+- if not mapping.has_key(str(key)):
++ if str(key) not in mapping:
+ mapping[str(key)] = [(aln[1], aln[2],aln[-1], 1-int(aln[0] == 'n'))]
+ mapping[str(key)+'\''] = [(aln[2], aln[1],aln[-1], int(aln[0] == 'n'))]
+ else:
+--- a/scripts/run_parse_alignment.py
++++ b/scripts/run_parse_alignment.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import sys
+ import os
+ import subprocess
+@@ -15,4 +15,4 @@ stream = subprocess.Popen(["LAshow", fil
+ alignments = parse_alignment(stream.stdout) # generator
+
+ for alignment in alignments:
+- print alignment
++ print(alignment)
+--- a/scripts/run_parse_read.py
++++ b/scripts/run_parse_read.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys
+ import os
+@@ -15,6 +15,6 @@ stream = subprocess.Popen(["DBshow", fil
+ reads = parse_read(stream.stdout) # generator
+
+ for read in reads:
+- print read
++ print(read)
+
+ #print result
+--- a/scripts/split_las.py
++++ b/scripts/split_las.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import os
+ import argparse
+--- a/scripts/unitig.py
++++ b/scripts/unitig.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import networkx as nx
+ import sys
+ import itertools
+@@ -7,7 +7,7 @@ filename = sys.argv[1]
+ outfile = filename.split('.')[0] + ".edges.list"
+
+ g = nx.read_graphml(filename)
+-print nx.info(g)
++print(nx.info(g))
+
+
+ def get_circle(g,node,vertices_of_interest):
+@@ -20,8 +20,8 @@ def get_circle(g,node,vertices_of_intere
+ try:
+ assert len(g.successors(cur_vertex)) == 1
+ except:
+- print g.successors(cur_vertex), cur_vertex, node
+- print cur_vertex in vertices_of_interest
++ print(g.successors(cur_vertex), cur_vertex, node)
++ print(cur_vertex in vertices_of_interest)
+ raise
+ successor = g.successors(cur_vertex)[0]
+ cur_vertex = successor
+@@ -43,7 +43,7 @@ def get_unitigs(g):
+ vertices_used = set(vertices_of_interest)
+ for start_vertex in vertices_of_interest:
+ first_out_vertices = g.successors(start_vertex)
+- print first_out_vertices
++ print(first_out_vertices)
+ for vertex in first_out_vertices:
+ cur_path = [start_vertex]
+ cur_vertex = vertex
+@@ -57,8 +57,8 @@ def get_unitigs(g):
+ vertices_used = vertices_used.union(set(cur_path))
+ paths.append(cur_path)
+
+- print len(node_set)
+- print len(vertices_used)
++ print(len(node_set))
++ print(len(vertices_used))
+
+ while len(node_set-vertices_used) > 0:
+ node = list(node_set-vertices_used)[0]
+@@ -70,15 +70,15 @@ def get_unitigs(g):
+ vertices_used = vertices_used.union(set(path))
+ if len(path) > 1:
+ paths.append(path)
+- print len(paths)
++ print(len(paths))
+ # print paths
+- print "paths"
++ print("paths")
+ return paths
+
+
+ paths = get_unitigs(g)
+
+-print len(paths)
++print(len(paths))
+
+ h = nx.DiGraph()
+ for i, path in enumerate(paths):
+@@ -89,7 +89,7 @@ vertices_of_interest = set([x for x in g
+ for vertex in vertices_of_interest:
+ successors = [x for x in h.nodes() if h.node[x]['path'][0] == vertex]
+ predecessors = [x for x in h.nodes() if h.node[x]['path'][-1] == vertex]
+- print successors,predecessors
++ print(successors,predecessors)
+ assert len(successors)==1 or len(predecessors)==1
+ for succ, pred in itertools.product(successors,predecessors):
+ h.add_edge(pred,succ)
+--- a/utils/run.sh
++++ b/utils/run.sh
+@@ -15,14 +15,14 @@ hinging --las $1.las --db $1 --config ~/
+
+ echo "Running Visualise"
+
+-python ~/AwesomeAssembler/scripts/Visualise_graph.py $1.edges.hinges hinge_list.txt
++python3 /usr/lib/hinge/Visualise_graph.py $1.edges.hinges hinge_list.txt
+
+ echo "Running Condense"
+
+-python ~/AwesomeAssembler/scripts/condense_graph.py $1.edges.hinges
++python3 /usr/lib/hinge/condense_graph.py $1.edges.hinges
+
+ echo "Putting ground truth and condensing"
+ if [ -e "$1.mapping.1.json" ]
+ then
+- python ~/AwesomeAssembler/scripts/condense_graph_with_aln_json.py $1.edges.hinges $1.mapping.1.json
+-fi
+\ No newline at end of file
++ python3 /usr/lib/hinge/condense_graph_with_aln_json.py $1.edges.hinges $1.mapping.1.json
++fi
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
external-spdlog.patch
libspdlog-14.0.patch
libspdlog-1:1.3.0
+2to3.patch
View it on GitLab: https://salsa.debian.org/med-team/hinge/compare/166303bb54b1e0e113d13a9286cd1635ec074d57...b21be0eeb81b0f0f78baca0f6f5030ad89314c8e
--
View it on GitLab: https://salsa.debian.org/med-team/hinge/compare/166303bb54b1e0e113d13a9286cd1635ec074d57...b21be0eeb81b0f0f78baca0f6f5030ad89314c8e
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