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Yoann DUFRESNE
linked reads molecule ordering
Commits
b82c96d6
Commit
b82c96d6
authored
Aug 20, 2019
by
Yoann Dufresne
Browse files
update tests
parent
04e7e460
Changes
1
Hide whitespace changes
Inline
Side-by-side
tests/d2_graph_test.py
View file @
b82c96d6
...
...
@@ -33,13 +33,11 @@ class TestD2Graph(unittest.TestCase):
else
:
self
.
assertEqual
(
1
,
len
(
d2
.
index
[
dmer
]))
def
test_linear_d2_construction
(
self
):
for
d
in
range
(
1
,
10
):
size
=
2
*
d
+
3
index_k
=
2
*
d
-
1
G
=
gm
.
generate_d_graph_chain
(
size
,
d
)
d2
=
D2Graph
(
G
)
d2
.
construct_from_barcodes
(
index_size
=
index_k
,
verbose
=
False
)
...
...
@@ -49,7 +47,7 @@ class TestD2Graph(unittest.TestCase):
self
.
assertEqual
(
awaited_d_num
,
len
(
d2
.
all_d_graphs
))
# Test index
awaited_index_size
=
comb
(
2
*
d
+
1
,
index_k
)
+
(
size
-
(
2
*
d
+
1
))
*
comb
(
2
*
d
,
index_k
-
1
)
awaited_index_size
=
comb
(
2
*
d
+
1
,
index_k
)
+
(
size
-
(
2
*
d
+
1
))
*
comb
(
2
*
d
,
index_k
-
1
)
if
len
(
d2
.
index
)
!=
awaited_index_size
:
dmers
=
[
list
(
x
)
for
x
in
d2
.
index
]
dmers
=
[
str
(
x
)
for
x
in
dmers
if
len
(
x
)
!=
len
(
frozenset
(
x
))]
...
...
@@ -59,15 +57,15 @@ class TestD2Graph(unittest.TestCase):
# Test connectivity
# Center node names
c1
=
d
c2
=
d
+
1
c3
=
d
+
2
c2
=
d
+
1
c3
=
d
+
2
# Connectivity matrix
awaited_distances
=
{
c1
:{
c2
:
2
,
c3
:
4
},
c2
:{
c1
:
2
,
c3
:
2
},
c3
:{
c1
:
4
,
c2
:
2
}
c1
:
{
c2
:
2
,
c3
:
4
},
c2
:
{
c1
:
2
,
c3
:
2
},
c3
:
{
c1
:
4
,
c2
:
2
}
}
for
x
,
y
,
data
in
d2
.
edges
(
data
=
True
):
dg1
=
d2
.
node_by_idx
[
x
]
dg2
=
d2
.
node_by_idx
[
y
]
...
...
@@ -81,11 +79,10 @@ class TestD2Graph(unittest.TestCase):
# for idx2, dist in neighbors.items():
# dg2 = d2.node_by_idx[idx2]
# awaited_dist = awaited_distances[dg1.center][dg2.center]
# self.assertEqual(dist, awaited_dist)
def
test_reloading
(
self
):
# Parameters
d
=
3
...
...
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