All tests

tests/context.py

@@ -7,3 +7,4 @@ import sys
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__),
                                                 '../debruijn')))
 import debruijn
+#import debruijn_comp

tests/test.fna

@@ -0,0 +1,8 @@
+>contig_0 len=8
+TCAGCGAT
+>contig_1 len=8
+TCAGCGAA
+>contig_2 len=8
+ACAGCGAT
+>contig_3 len=8
+ACAGCGAA

tests/test_characteristics.py

@@ -0,0 +1,59 @@
+"""Tests for graph characteristic"""
+import pytest
+import os
+import networkx as nx
+import hashlib
+from .context import debruijn
+#from .context import debruijn_comp
+from debruijn import get_starting_nodes
+from debruijn import get_sink_nodes
+from debruijn import get_contigs
+from debruijn import save_contigs
+
+
+def test_get_starting_nodes():
+    graph = nx.DiGraph()
+    graph.add_edges_from([(1, 2), (3, 2), (2, 4), (4, 5), (5, 6), (5, 7)])
+    nodes = get_starting_nodes(graph)    
+    assert len(nodes) == 2
+    assert 1 in nodes
+    assert 3 in nodes
+
+def test_get_sink_nodes():
+    graph = nx.DiGraph()
+    graph.add_edges_from([(1, 2), (3, 2), (2, 4), (4, 5), (5, 6), (5, 7)])
+    nodes = get_sink_nodes(graph)
+    assert len(nodes) == 2
+    assert 6 in nodes
+    assert 7 in nodes
+
+def test_get_contigs():
+    graph = nx.DiGraph()
+    graph.add_edges_from([("TC", "CA"), ("AC", "CA"), ("CA", "AG"), ("AG", "GC"), ("GC", "CG"), ("CG", "GA"), ("GA", "AT"), ("GA", "AA")])
+    contig_list = get_contigs(graph, ["TC", "AC"], ["AT" , "AA"])
+    results = ["TCAGCGAT", "TCAGCGAA", "ACAGCGAT", "ACAGCGAA"]
+    assert len(contig_list) == 4
+    for contig in contig_list:
+        assert contig[0] in results
+        assert contig[1] == 8
+
+
+# def test_get_contigs_comp():
+#     graph = nx.DiGraph()
+#     graph.add_edges_from([(("AG", "TC"), ("CA", "GT")), (("AC", "TG"), ("CA", "GT")), (("CA", "GT"), ("AG", "TC")), 
+#         (("AG", "TC"), ("CG", "GC")), (("CG", "GC"), ("CG", "GC")), (("CG", "GC"), ("CT", "GA")), (("CT", "GA"), ("AT", "TC")), 
+#         (("CT", "GA"), ("AA", "TT"))])
+#     contig_list = get_contigs(graph, ["TC", "AC"], ["AT" , "AA"])
+#     results = ["TCAGCGAT", "TCAGCGAA", "ACAGCGAT", "ACAGCGAA"]
+#     assert len(contig_list) == 4
+#     for contig in contig_list:
+#         assert contig[0] in results
+#         assert contig[1] == 8
+
+
+def test_save_contigs():
+    test_file = os.path.abspath(os.path.join(os.path.dirname(__file__), "test.fna"))
+    contig = [("TCAGCGAT", 8), ("TCAGCGAA",8), ("ACAGCGAT", 8), ("ACAGCGAA", 8)]
+    save_contigs(contig, test_file)
+    with open(test_file, 'rb') as contig_test:
+        assert hashlib.md5(contig_test.read()).hexdigest() == "ca84dfeb5d58eca107e34de09b3cc997"

tests/test_construction_debruijn.py

@@ -4,6 +4,7 @@ import os
 import networkx as nx
 import pickle
 from .context import debruijn
+#from .context import debruijn_comp
 from debruijn import read_fastq
 from debruijn import cut_kmer
 from debruijn import build_kmer_dict
@@ -48,4 +49,21 @@ def test_build_graph():
     assert graph.number_of_edges() == 4
     assert "AG" in graph
     assert "GA" in graph
-    assert graph.edges["AG", "GA"]['weight'] == 2
+    assert graph.edges["AG", "GA"]['weight'] == 2
+
+# def test_build_graph_comp():
+#     file = open(os.path.abspath(os.path.join(os.path.dirname(__file__), "kmer_comp.pck")),'rb')
+#     kmer_dict = pickle.load(file)
+#     graph = build_graph(kmer_dict)
+#     #TCAGAGA
+#     #TCA  TC CA
+#     #CAG CA AG
+#     #AGA AG GA
+#     #GAG GA AG
+#     #AGA AG GA
+#     # ((TC, AG), (CA, GT)), (CA, AG), (AG
+#     assert graph.number_of_nodes() == 4
+#     assert graph.number_of_edges() == 3
+#     assert "AG" in graph
+#     assert "GA" in graph
+#     assert graph.edges["AG", "GA"]['weight'] == 2

tests/test_decision.py

@@ -0,0 +1,170 @@
+"""Tests decision"""
+import pytest
+import os
+import networkx as nx
+import statistics
+from .context import debruijn
+#from .context import debruijn_comp
+from debruijn import std
+from debruijn import path_average_weight
+from debruijn import remove_paths
+from debruijn import select_best_path
+from debruijn import solve_bubble
+from debruijn import simplify_bubbles
+from debruijn import solve_entry_tips
+from debruijn import solve_out_tips
+
+def test_std():
+    assert round(std([9, 5, 15, 20]), 1) == 6.6
+
+
+def test_path_weight():
+    graph = nx.DiGraph()
+    graph.add_weighted_edges_from([(1, 2, 5), (3, 2, 10), (2, 4, 10), (4, 5, 3), 
+                                   (5, 6, 10), (5, 7, 10)])
+    assert path_average_weight(graph, [1, 2, 4, 5] ) == 6.0
+
+def test_remove_paths():
+    graph_1 = nx.DiGraph()
+    graph_2 = nx.DiGraph()
+    graph_3 = nx.DiGraph()
+    graph_4 = nx.DiGraph()
+    graph_1.add_edges_from([(1, 2), (3, 2), (2, 4), (4, 5), (5, 6), (5, 7)])
+    graph_2.add_edges_from([(1, 2), (3, 2), (2, 4), (4, 5), (5, 6), (5, 7)])
+    graph_3.add_edges_from([(1, 2), (3, 2), (2, 4), (4, 5), (5, 6), (5, 7)])
+    graph_4.add_edges_from([(1, 2), (3, 2), (2, 4), (4, 5), (5, 6), (5, 7)])
+    graph_1 = remove_paths(graph_1, [(1,2)], True, False)
+    graph_2 = remove_paths(graph_2, [(5,7)], False, True)
+    graph_3 = remove_paths(graph_3, [(2,4,5)], False, False)
+    graph_4 = remove_paths(graph_4, [(2,4,5)], True, True)
+    assert (1,2) not in graph_1.edges()
+    assert (3,2) in graph_1.edges()
+    assert (5,7) not in graph_2.edges()
+    assert (5,6) in graph_2.edges()
+    assert 4 not in graph_3.nodes()
+    assert (2,4) not in graph_4.edges()
+    assert (4, 5) not in graph_4.edges()
+    assert 2 not in graph_4.nodes()
+    assert 4 not in graph_4.nodes()
+    assert 5 not in graph_4.nodes()
+
+def test_select_best_path():
+    graph_1 = nx.DiGraph()
+    graph_1.add_edges_from([(1, 2), (3, 2), (2, 4), (4, 5), (5, 6), (5, 7)])
+    graph_1 = select_best_path(graph_1, [[1,2], [3,2]], [1, 1], [5, 10], delete_entry_node=True)
+    assert (1,2) not in graph_1.edges()
+    assert (3,2) in graph_1.edges()
+    assert 1 not in graph_1.nodes()
+    graph_2 = nx.DiGraph()
+    graph_2.add_edges_from([(1, 2), (3, 2), (2, 4), (4, 5), (5, 6), (5, 7) , (7, 8)])
+    graph_2 = select_best_path(graph_1, [[5, 6], [5, 7, 8]], [1, 2], [13, 10], delete_sink_node=True)
+    assert (5,7) not in graph_2.edges()
+    assert (7,8) not in graph_2.edges()
+    assert (5,6) in graph_2.edges()
+    assert 7 not in graph_2.nodes()
+    assert 8 not in graph_2.nodes()
+    #Select heavier
+    graph_3 = nx.DiGraph()
+    graph_3.add_edges_from([(1, 2), (3, 2), (2, 4), (4, 5), (2, 8), (8, 9),
+                            (9, 5), (5, 6), (5, 7)])
+    graph_3 = select_best_path(graph_3, [[2, 4, 5], [2, 8, 9, 5]],
+                                         [1, 4], [13, 10])
+    assert (2,8) not in graph_3.edges()
+    assert (8,9) not in graph_3.edges()
+    assert (9,5) not in graph_3.edges()
+    assert (2,4) in graph_3.edges()
+    assert (4,5) in graph_3.edges()
+    assert 8 not in graph_3.nodes()
+    assert 9 not in graph_3.nodes()
+    assert 2 in graph_3.nodes()
+    assert 5 in graph_3.nodes()
+    # Select longest
+    graph_4 = nx.DiGraph()
+    graph_4.add_edges_from([(1, 2), (3, 2), (2, 4), (4, 5), (2, 8), (8, 9), 
+                            (9, 5), (5, 6), (5, 7)])
+    graph_4 = select_best_path(graph_4, [[2, 4, 5], [2, 8, 9, 5]],
+                                         [1, 4], [10, 10])
+    assert (2,4) not in graph_4.edges()
+    assert (4,5) not in graph_4.edges()
+    assert (2,8) in graph_4.edges()
+    assert (8,9) in graph_4.edges()
+    assert (9,5) in graph_4.edges()
+    # Select random
+    graph_5 = nx.DiGraph()
+    graph_5.add_edges_from([(1, 2), (3, 2), (2, 4), (4, 5), (2, 8), (8, 9),
+                            (9, 5), (5, 6), (5, 7)])
+    graph_5 = select_best_path(graph_5, [[2, 4, 5], [2, 8, 9, 5]],
+                                         [1, 4], [10, 10])
+
+def test_solve_bubble():
+    graph_1 = nx.DiGraph()
+    graph_1.add_weighted_edges_from([(1, 2, 10), (3, 2, 10), (2, 4, 15), 
+                                     (4, 5, 15), (2, 10,10), (10, 5,10),
+                                     (2, 8, 3), (8, 9, 3), (9, 5, 3),
+                                     (5, 6, 10), (5, 7, 10)])
+    graph_1 = solve_bubble(graph_1, 2, 5)
+    assert (2,8) not in graph_1.edges()
+    assert (8,9) not in graph_1.edges()
+    assert (9,5) not in graph_1.edges()
+    assert (2,10) not in graph_1.edges()
+    assert (10, 5) not in graph_1.edges()
+    assert (2,4) in graph_1.edges()
+    assert (4,5) in graph_1.edges()
+    assert 8 not in graph_1.nodes()
+    assert 9 not in graph_1.nodes()
+    assert 10 not in graph_1.nodes()
+    assert 2 in graph_1.nodes()
+    assert 5 in graph_1.nodes()
+    graph_2 = nx.DiGraph()
+    graph_2.add_weighted_edges_from([(1, 2, 10), (3, 2, 10), (2, 4, 10), 
+                                     (4, 5, 10), (2, 10,10), (10, 5,10),
+                                     (2, 8, 10), (8, 9, 10), (9, 5, 10),
+                                     (5, 6, 10), (5, 7, 10)])
+    graph_2 = solve_bubble(graph_2, 2, 5)
+    assert (2,4) not in graph_2.edges()
+    assert (4,5) not in graph_2.edges()
+    assert (2,10) not in graph_1.edges()
+    assert (10, 5) not in graph_1.edges()
+    assert (2,8) in graph_2.edges()
+    assert (8,9) in graph_2.edges()
+    assert (9,5) in graph_2.edges()
+
+
+def test_simplify_bubbles():
+    graph_1 = nx.DiGraph()
+    graph_1.add_weighted_edges_from([(3, 2, 10), (2, 4, 15), (4, 5, 15),
+                                     (2, 10,10), (10, 5,10), (2, 8, 3),
+                                     (8, 9, 3), (9, 5, 3), (5, 6, 10),
+                                     (5, 7, 10)])
+    graph_1 = simplify_bubbles(graph_1)
+    assert (2,8) not in graph_1.edges()
+    assert (8,9) not in graph_1.edges()
+    assert (9,5) not in graph_1.edges()
+    assert (2,10) not in graph_1.edges()
+    assert (10, 5) not in graph_1.edges()
+
+def test_solve_entry_tips():
+    graph_1 = nx.DiGraph()
+    graph_1.add_weighted_edges_from([(1, 2, 10), (3, 2, 2), (2, 4, 15), (4, 5, 15)])
+    graph_1 = solve_entry_tips(graph_1, [1, 3])  
+    assert (3, 2) not in graph_1.edges()
+    assert (1, 2) in graph_1.edges()
+    graph_2 = nx.DiGraph()
+    graph_2.add_weighted_edges_from([(1, 2, 2), (6, 3, 2), (3, 2, 2),
+                                     (2, 4, 15), (4, 5, 15)])
+    graph_2 = solve_entry_tips(graph_2, [1, 6])  
+    assert (1, 2) not in graph_2.edges()
+    assert (6, 3) in graph_2.edges()
+    assert (3, 2) in graph_2.edges()
+
+def test_solve_out_tips():
+    graph_1 = nx.DiGraph()
+    graph_1.add_weighted_edges_from([(1, 2, 15), (2, 3, 15), (4, 5, 15), (4, 6, 2)])
+    graph_1 = solve_out_tips(graph_1, [5, 6])  
+    assert (4, 6) not in graph_1.edges()
+    assert (4, 5) in graph_1.edges()  
+    graph_2 = nx.DiGraph()
+    graph_2.add_weighted_edges_from([(1, 2, 15), (2, 3, 15), (4, 5, 2), (4, 6, 2) , (6, 7, 2)])
+    graph_2 = solve_out_tips(graph_2, [5, 7])  
+    assert (4, 5) not in graph_2.edges()
+    assert (6, 7) in graph_2.edges()