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Huang Di
treebuilder
Commits
ed27460a
Commit
ed27460a
authored
Jul 07, 2023
by
Huang Di
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gene flow proportion block list, display threshold
parent
f47a1c00
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2 changed files
with
24 additions
and
5 deletions
+24
-5
main.py
+8
-3
treebuilder.py
+16
-2
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main.py
View file @
ed27460a
...
@@ -17,17 +17,22 @@ args = {
...
@@ -17,17 +17,22 @@ args = {
'threshold2'
:
0
,
# gene flow display threshold
'threshold2'
:
0
,
# gene flow display threshold
'threshold3'
:
3
,
# gene flow merge threshold
'threshold3'
:
3
,
# gene flow merge threshold
'bidirectional'
:
True
,
# calculate the reversed gene flow
'bidirectional'
:
True
,
# calculate the reversed gene flow
'calculate_pd'
:
Fals
e
,
# calculate the gene flow confidence
'calculate_pd'
:
Tru
e
,
# calculate the gene flow confidence
'data_path'
:
'data/test.log'
,
'data_path'
:
'data/test.log'
,
'save_path'
:
'pictures/tree
2
.png'
,
'save_path'
:
'pictures/tree.png'
,
'draw_gene_flow'
:
True
,
'draw_gene_flow'
:
True
,
'gene_flow_display_confidence'
:
0.7
,
'target_block_list'
:
[
'Tianyuan'
],
's1_block_list'
:
[
'Boshan'
],
# 'target_block_list': [],
# 's1_block_list': [],
}
}
populations
=
[
'Kostenki14'
,
populations
=
[
'Kostenki14'
,
'Tianyuan'
,
'Tianyuan'
,
'AR19K'
,
'AR19K'
,
'AR14K'
,
'AR14K'
,
'Zongri5
.
1k'
,
'Zongri5
_
1k'
,
'Boshan'
,
'Boshan'
,
'Qihe3'
,
'Qihe3'
,
'Donghulin'
,
'Donghulin'
,
...
...
treebuilder.py
View file @
ed27460a
from
itertools
import
combinations
from
itertools
import
combinations
from
data_structures
import
UnionFindSet
,
Graph
from
data_structures
import
UnionFindSet
,
Graph
from
anytree
import
Node
,
PreOrderIter
from
anytree
import
Node
,
PreOrderIter
,
RenderTree
from
anytree.exporter
import
DotExporter
from
anytree.exporter
import
DotExporter
from
collections
import
defaultdict
from
collections
import
defaultdict
# from sklearn.linear_model import LinearRegression
# from sklearn.linear_model import LinearRegression
...
@@ -405,6 +405,8 @@ class TreeBuilder(object):
...
@@ -405,6 +405,8 @@ class TreeBuilder(object):
bidirectional
=
kwargs
.
get
(
'bidirectional'
,
True
)
bidirectional
=
kwargs
.
get
(
'bidirectional'
,
True
)
calculate_pd
=
kwargs
.
get
(
'calculate_pd'
,
False
)
calculate_pd
=
kwargs
.
get
(
'calculate_pd'
,
False
)
tar_block_list
=
kwargs
.
get
(
'target_block_list'
,
[])
s1_block_list
=
kwargs
.
get
(
's1_block_list'
,
[])
# calculate_m1('Dushan', 'Baojianshan')
# calculate_m1('Dushan', 'Baojianshan')
# calculate_m1('Baojianshan', 'Dushan')
# calculate_m1('Baojianshan', 'Dushan')
# calculate_m1('Boshan', 'Dushan')
# calculate_m1('Boshan', 'Dushan')
...
@@ -413,10 +415,12 @@ class TreeBuilder(object):
...
@@ -413,10 +415,12 @@ class TreeBuilder(object):
print
(
'Calculating gene flows...'
)
print
(
'Calculating gene flows...'
)
gf_cnt
=
0
gf_cnt
=
0
for
s2
,
tar
in
gene_flow
:
for
s2
,
tar
in
gene_flow
:
if
tar
in
tar_block_list
:
continue
propotion
[(
s2
,
tar
)]
=
[]
propotion
[(
s2
,
tar
)]
=
[]
if
(
s2
,
tar
)
not
in
self
.
s1_record
:
if
(
s2
,
tar
)
not
in
self
.
s1_record
:
continue
continue
for
s1
in
self
.
s1_record
[(
s2
,
tar
)]:
for
s1
in
self
.
s1_record
[(
s2
,
tar
)]:
if
s1
in
s1_block_list
:
continue
if
DEBUG
:
if
DEBUG
:
print
(
'-----------------------------------------------'
)
print
(
'-----------------------------------------------'
)
# pd = False to make it fast
# pd = False to make it fast
...
@@ -442,10 +446,12 @@ class TreeBuilder(object):
...
@@ -442,10 +446,12 @@ class TreeBuilder(object):
if
bidirectional
:
if
bidirectional
:
print
(
'Calculating reversed gene flows...'
)
print
(
'Calculating reversed gene flows...'
)
for
tar
,
s2
in
gene_flow
:
for
tar
,
s2
in
gene_flow
:
if
tar
in
tar_block_list
:
continue
propotion
[(
s2
,
tar
)]
=
[]
propotion
[(
s2
,
tar
)]
=
[]
if
(
s2
,
tar
)
not
in
self
.
s1_record
:
if
(
s2
,
tar
)
not
in
self
.
s1_record
:
continue
continue
for
s1
in
self
.
s1_record
[(
s2
,
tar
)]:
for
s1
in
self
.
s1_record
[(
s2
,
tar
)]:
if
s1
in
s1_block_list
:
continue
mix_bc
,
m_pd_bc
=
calculate_m1
(
s1
,
tar
,
s2
)
mix_bc
,
m_pd_bc
=
calculate_m1
(
s1
,
tar
,
s2
)
# mix_a1b, mix_pd_a1b = calculate_m1(s2, tar, s1)
# mix_a1b, mix_pd_a1b = calculate_m1(s2, tar, s1)
# print('mix_bc, mix_a1b', mix_bc, mix_a1b)
# print('mix_bc, mix_a1b', mix_bc, mix_a1b)
...
@@ -468,6 +474,8 @@ class TreeBuilder(object):
...
@@ -468,6 +474,8 @@ class TreeBuilder(object):
print
(
mat
.
format
(
's2'
,
'tar'
,
's1'
,
'mix'
,
'm_pd'
))
print
(
mat
.
format
(
's2'
,
'tar'
,
's1'
,
'mix'
,
'm_pd'
))
mat
=
"{:10}
\t
{:10}
\t
{:10}
\t
{:.3f}
\t
{:.3f}"
mat
=
"{:10}
\t
{:10}
\t
{:10}
\t
{:.3f}
\t
{:.3f}"
m_pd_display_threshold
=
kwargs
.
get
(
'gene_flow_display_confidence'
,
0.0
)
gene_flows_checked_by_propotion
=
[]
gene_flows_checked_by_propotion
=
[]
for
gene_flow
,
m1s
in
propotion
.
items
():
for
gene_flow
,
m1s
in
propotion
.
items
():
s2
,
tar
=
gene_flow
s2
,
tar
=
gene_flow
...
@@ -476,7 +484,10 @@ class TreeBuilder(object):
...
@@ -476,7 +484,10 @@ class TreeBuilder(object):
# print(s2, tar, s1, mix, m_pd)
# print(s2, tar, s1, mix, m_pd)
print
(
mat
.
format
(
s2
,
tar
,
s1
,
mix
,
m_pd
))
print
(
mat
.
format
(
s2
,
tar
,
s1
,
mix
,
m_pd
))
if
(
s2
,
tar
)
not
in
gene_flows_checked_by_propotion
:
if
(
s2
,
tar
)
not
in
gene_flows_checked_by_propotion
:
gene_flows_checked_by_propotion
.
append
((
s2
,
tar
))
if
not
(
calculate_pd
and
m_pd
<
m_pd_display_threshold
):
gene_flows_checked_by_propotion
.
append
((
s2
,
tar
))
print
(
',,,'
,
gene_flows_checked_by_propotion
)
print
(
m_pd_display_threshold
)
return
gene_flows_checked_by_propotion
return
gene_flows_checked_by_propotion
def
calculate_propotion_bak2
(
self
,
gene_flow
,
order
,
visited_leaves
,
bidirectional
=
True
):
def
calculate_propotion_bak2
(
self
,
gene_flow
,
order
,
visited_leaves
,
bidirectional
=
True
):
...
@@ -693,6 +704,9 @@ class TreeBuilder(object):
...
@@ -693,6 +704,9 @@ class TreeBuilder(object):
if
print_gene_flow
:
if
print_gene_flow
:
for
l1
,
l2
in
self
.
gene_flow
:
for
l1
,
l2
in
self
.
gene_flow
:
options
.
append
(
"
%
s ->
%
s [color=red]"
%
(
l1
,
l2
))
options
.
append
(
"
%
s ->
%
s [color=red]"
%
(
l1
,
l2
))
print
(
self
.
populations
)
print
(
self
.
relations
)
print
(
RenderTree
(
self
.
root
))
return
DotExporter
(
self
.
root
,
options
=
options
)
return
DotExporter
(
self
.
root
,
options
=
options
)
def
export_dot
(
self
,
filename
,
print_gene_flow
=
True
):
def
export_dot
(
self
,
filename
,
print_gene_flow
=
True
):
...
...
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