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debruijn-tp
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All tests

master
Amine GHOZLANE 2019-10-21 13:11:45 +02:00
parent 7d338cec02
commit 9055bb490a
6 changed files with 257 additions and 1 deletions
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1
tests/context.py
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@ -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

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tests/kmer_comp.pck Normal file
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8
tests/test.fna Normal file
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@ -0,0 +1,8 @@
>contig_0 len=8
TCAGCGAT
>contig_1 len=8
TCAGCGAA
>contig_2 len=8
ACAGCGAT
>contig_3 len=8
ACAGCGAA

59
tests/test_characteristics.py Normal file
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@ -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"

20
tests/test_construction_debruijn.py
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@ -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

170
tests/test_decision.py Normal file
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@ -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()