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Yoann DUFRESNE
linked reads molecule ordering
Commits
b79c63d1
Commit
b79c63d1
authored
Jan 24, 2020
by
rchikhi
Browse files
barcode graphe generation from genomes tuning
parent
56839d4c
Changes
2
Hide whitespace changes
Inline
Side-by-side
deconvolution/main/generate_genome_molecule_graph.py
View file @
b79c63d1
...
...
@@ -19,27 +19,42 @@ def parse_arguments():
return
args
def
compute_ovl_length
(
s1
,
e1
,
s2
,
e2
):
if
s1
>
s2
:
s1
,
e1
,
s2
,
e2
=
s2
,
e2
,
s1
,
e1
return
e1
-
s2
def
is_contained
(
itree
,
start
,
end
):
for
itv
in
itree
.
overlap
(
start
,
end
):
start2
,
end2
=
itv
.
begin
,
itv
.
end
if
start2
<=
start
and
end2
>=
end
:
return
True
return
False
def
generate_graph
(
nb_molecules
,
genome_size
,
avg_mol_size
,
min_mol_ovl
,
rnd_seed
=
None
):
# Reproducibility
if
rnd_seed
!=
-
1
:
np
.
random
.
seed
(
rnd_seed
)
G
=
nx
.
Graph
()
# generate molecules according to similar principle as LRSM
# but in addition make sure they're not contained in each other
molecules
=
dict
()
# mol index: (start,end)
itree
=
IntervalTree
()
for
idx
in
range
(
nb_molecules
):
while
True
:
# to avoid contained molecules
G
.
add_node
(
idx
)
#pick a starting position (follows LRSIM)
start
_pos
=
np
.
random
.
randint
(
0
,
genome_size
)
start
=
np
.
random
.
randint
(
0
,
genome_size
)
#pick a fragment size (follows LRSIM)
molecule_size
=
np
.
random
.
poisson
(
avg_mol_size
)
print
(
"molecule"
,
idx
,
"start"
,
start_pos
,
"end"
,
start_pos
+
molecule_size
)
molecules
[
idx
]
=
(
start_pos
,
start_pos
+
molecule_size
)
# compute overlaps between molecules
itree
=
IntervalTree
()
for
idx
in
molecules
:
start
,
end
=
molecules
[
idx
]
itree
.
addi
(
start
,
end
,
idx
)
end
=
start
+
molecule_size
if
is_contained
(
itree
,
start
,
end
):
continue
print
(
"molecule"
,
idx
,
"start"
,
start
,
"end"
,
end
)
molecules
[
idx
]
=
(
start
,
end
)
itree
.
addi
(
start
,
end
,
idx
)
break
# create graph edges corresponding to molecules overlaps
for
idx
in
molecules
:
...
...
@@ -47,6 +62,10 @@ def generate_graph(nb_molecules, genome_size, avg_mol_size, min_mol_ovl, rnd_see
for
itv
in
itree
.
overlap
(
start
,
end
):
other_idx
=
itv
.
data
if
idx
==
other_idx
:
continue
start2
,
end2
=
itv
.
begin
,
itv
.
end
ovl_length
=
compute_ovl_length
(
start
,
end
,
start2
,
end2
)
#print("overlap length",ovl_length)
if
ovl_length
<
min_mol_ovl
:
continue
G
.
add_edge
(
idx
,
other_idx
)
return
G
...
...
requirements.txt
View file @
b79c63d1
...
...
@@ -4,3 +4,4 @@ bidict
pytest
scipy
python-louvain
intervaltree
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