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mrdna
Commits
6f40a20c
Commit
6f40a20c
authored
Feb 27, 2020
by
cmaffeo2
Browse files
Fixed edge case with model_from_lists when circular helices have crossovers near their 'ends'
parent
5e2b9f05
Changes
2
Hide whitespace changes
Inline
Side-by-side
mrdna/readers/segmentmodel_from_lists.py
View file @
6f40a20c
...
@@ -117,45 +117,49 @@ def basepairs_and_stacks_to_helixmap(basepairs,stacks_above):
...
@@ -117,45 +117,49 @@ def basepairs_and_stacks_to_helixmap(basepairs,stacks_above):
hid
+=
1
hid
+=
1
## Create "helix" for each circular segment
## Create "helix" for each circular segment
intrahelical
=
[]
processed
=
set
()
processed
=
set
()
unclaimed_bases
=
np
.
where
(
(
basepairs
>=
0
)
*
(
helixmap
==
-
1
)
)[
0
]
unclaimed_bases
=
np
.
where
(
(
basepairs
>=
0
)
*
(
helixmap
==
-
1
)
)[
0
]
for
nt0
in
unclaimed_bases
:
for
nt0
in
unclaimed_bases
:
if
nt0
in
processed
:
continue
if
nt0
in
processed
:
continue
nt
=
nt0
nt
=
nt0
all_nts
=
[
nt
]
all_nts
=
[
nt
]
rank
=
0
nt
=
nt0
bp
=
basepairs
[
nt
]
assert
(
helixmap
[
nt
]
==
-
1
)
assert
(
helixmap
[
bp
]
==
-
1
)
helixmap
[
nt
]
=
helixmap
[
bp
]
=
hid
helixrank
[
nt
]
=
helixrank
[
bp
]
=
rank
is_fwd
[
bp
]
=
0
rank
+=
1
processed
.
add
(
nt
)
processed
.
add
(
bp
)
counter
=
0
counter
=
0
while
stacks_above
[
nt
]
>=
0
:
while
stacks_above
[
nt
]
>=
0
:
lastnt
=
nt
nt
=
stacks_above
[
nt
]
nt
=
stacks_above
[
nt
]
bp
=
basepairs
[
nt
]
bp
=
basepairs
[
nt
]
if
nt
==
nt0
or
nt
==
basepairs
[
nt0
]:
intrahelical
.
append
((
lastnt
,
nt0
))
break
assert
(
bp
>=
0
)
assert
(
bp
>=
0
)
assert
(
helixmap
[
nt
]
==
-
1
)
assert
(
helixmap
[
nt
]
==
-
1
)
assert
(
helixmap
[
bp
]
==
-
1
)
assert
(
helixmap
[
bp
]
==
-
1
)
if
nt
==
nt0
:
helixmap
[
nt
]
=
helixmap
[
bp
]
=
hid
break
helixrank
[
nt
]
=
helixrank
[
bp
]
=
rank
is_fwd
[
bp
]
=
0
all_nts
.
append
(
nt
)
processed
.
add
(
nt
)
processed
.
add
(
bp
)
if
counter
>
1e6
:
rank
+=
1
raise
Exception
(
"DNA is apparently too long; probably there is something wrong with the structure"
)
hid
+=
1
counter
+=
1
## Split circular helix into two groups (TODO: fix segmentmodel so that circular helices work and this is not needed)
for
group
in
(
all_nts
[:
len
(
all_nts
)
//
2
],
all_nts
[
len
(
all_nts
)
//
2
:]):
rank
=
0
for
nt
in
group
:
bp
=
basepairs
[
nt
]
is_fwd
[
bp
]
=
0
helixmap
[
nt
]
=
helixmap
[
bp
]
=
hid
helixrank
[
nt
]
=
helixrank
[
bp
]
=
rank
processed
.
add
(
nt
)
processed
.
add
(
bp
)
rank
+=
1
hid
+=
1
return
helixmap
,
helixrank
,
is_fwd
return
helixmap
,
helixrank
,
is_fwd
,
intrahelical
def
set_splines
(
seg
,
coordinate
,
hid
,
hmap
,
hrank
,
fwd
,
orientation
=
None
):
def
set_splines
(
seg
,
coordinate
,
hid
,
hmap
,
hrank
,
fwd
,
orientation
=
None
):
...
@@ -282,7 +286,7 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
...
@@ -282,7 +286,7 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
five_prime
=
_three_prime_list_to_five_prime
(
three_prime
)
five_prime
=
_three_prime_list_to_five_prime
(
three_prime
)
""" Build map of dsDNA helices and strands """
""" Build map of dsDNA helices and strands """
hmap
,
hrank
,
fwd
=
basepairs_and_stacks_to_helixmap
(
bps
,
stack
)
hmap
,
hrank
,
fwd
,
intrahelical
=
basepairs_and_stacks_to_helixmap
(
bps
,
stack
)
double_stranded_helices
=
np
.
unique
(
hmap
[
hmap
>=
0
])
double_stranded_helices
=
np
.
unique
(
hmap
[
hmap
>=
0
])
strands
,
strand_is_circular
=
_primes_list_to_strands
(
three_prime
,
five_prime
)
strands
,
strand_is_circular
=
_primes_list_to_strands
(
three_prime
,
five_prime
)
...
@@ -356,6 +360,7 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
...
@@ -356,6 +360,7 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
## Handle connections at the ends
## Handle connections at the ends
is_terminal1
=
(
nt1
,
f1
)
in
((
0
,
0
),(
seg1
.
num_nt
-
1
,
1
))
is_terminal1
=
(
nt1
,
f1
)
in
((
0
,
0
),(
seg1
.
num_nt
-
1
,
1
))
is_terminal2
=
(
nt2
,
f2
)
in
((
0
,
1
),(
seg2
.
num_nt
-
1
,
0
))
is_terminal2
=
(
nt2
,
f2
)
in
((
0
,
1
),(
seg2
.
num_nt
-
1
,
0
))
if
is_terminal1
or
is_terminal2
:
if
is_terminal1
or
is_terminal2
:
""" Re-evaluate condition for being terminal so that both
""" Re-evaluate condition for being terminal so that both
strands must be connected at end to have an 'intrahelical'
strands must be connected at end to have an 'intrahelical'
...
@@ -383,6 +388,19 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
...
@@ -383,6 +388,19 @@ def model_from_basepair_stack_3prime(coordinate, basepair, stack, three_prime,
seg
=
allSegments
[
hmap
[
r
]]
seg
=
allSegments
[
hmap
[
r
]]
seg
.
add_3prime
(
hrank
[
r
],
fwd
[
r
])
seg
.
add_3prime
(
hrank
[
r
],
fwd
[
r
])
## Add intrahelical connections to circular helical sections
for
nt0
,
nt1
in
intrahelical
:
seg
=
allSegments
[
hmap
[
nt0
]]
assert
(
seg
is
allSegments
[
hmap
[
nt1
]]
)
if
three_prime
[
nt0
]
>=
0
:
if
hmap
[
nt0
]
==
hmap
[
three_prime
[
nt0
]]:
seg
.
connect_end3
(
seg
.
start5
)
bp0
,
bp1
=
[
bps
[
nt
]
for
nt
in
(
nt0
,
nt1
)]
if
three_prime
[
bp1
]
>=
0
:
if
hmap
[
bp1
]
==
hmap
[
three_prime
[
bp1
]]:
seg
.
connect_start3
(
seg
.
end5
)
## Assign sequence
## Assign sequence
if
sequence
is
not
None
:
if
sequence
is
not
None
:
for
hid
in
range
(
len
(
allSegments
)):
for
hid
in
range
(
len
(
allSegments
)):
...
...
mrdna/segmentmodel.py
View file @
6f40a20c
...
@@ -98,7 +98,10 @@ class Location():
...
@@ -98,7 +98,10 @@ class Location():
on_fwd
=
"on_fwd_strand"
on_fwd
=
"on_fwd_strand"
else
:
else
:
on_fwd
=
"on_rev_strand"
on_fwd
=
"on_rev_strand"
return
"<Location {}.{}[{:.2f},{:d}]>"
.
format
(
self
.
container
.
name
,
self
.
type_
,
self
.
address
,
self
.
on_fwd_strand
)
try
:
return
"<Location {}.{}[{:d},{}]>"
.
format
(
self
.
container
.
name
,
self
.
type_
,
self
.
get_nt_pos
(),
on_fwd
)
except
:
return
"<Location {}.{}[{:.2f},{:d}]>"
.
format
(
self
.
container
.
name
,
self
.
type_
,
self
.
address
,
self
.
on_fwd_strand
)
class
Connection
():
class
Connection
():
""" Abstract base class for connection between two elements """
""" Abstract base class for connection between two elements """
...
@@ -1155,12 +1158,25 @@ class DoubleStrandedSegment(Segment):
...
@@ -1155,12 +1158,25 @@ class DoubleStrandedSegment(Segment):
c
=
self
.
nt_pos_to_contour
(
nt
)
c
=
self
.
nt_pos_to_contour
(
nt
)
assert
(
c
>=
0
and
c
<=
1
)
assert
(
c
>=
0
and
c
<=
1
)
loc
=
self
.
get_location_at
(
c
,
strands_fwd
[
0
])
if
nt
==
0
and
not
strands_fwd
[
0
]:
loc
=
self
.
start3
elif
nt
==
self
.
num_nt
-
1
and
strands_fwd
[
0
]:
loc
=
self
.
end3
else
:
loc
=
self
.
get_location_at
(
c
,
strands_fwd
[
0
])
c
=
other
.
nt_pos_to_contour
(
other_nt
)
c
=
other
.
nt_pos_to_contour
(
other_nt
)
# TODOTODO: may need to subtract or add a little depending on 3prime/5prime
# TODOTODO: may need to subtract or add a little depending on 3prime/5prime
assert
(
c
>=
0
and
c
<=
1
)
assert
(
c
>=
0
and
c
<=
1
)
other_loc
=
other
.
get_location_at
(
c
,
strands_fwd
[
1
])
if
other_nt
==
0
and
strands_fwd
[
1
]:
other_loc
=
other
.
start5
elif
other_nt
==
other
.
num_nt
-
1
and
not
strands_fwd
[
1
]:
other_loc
=
other
.
end5
else
:
other_loc
=
other
.
get_location_at
(
c
,
strands_fwd
[
1
])
self
.
_connect
(
other
,
Connection
(
loc
,
other_loc
,
type_
=
type_
))
self
.
_connect
(
other
,
Connection
(
loc
,
other_loc
,
type_
=
type_
))
if
nt_on_5prime
:
if
nt_on_5prime
:
loc
.
is_3prime_side_of_connection
=
False
loc
.
is_3prime_side_of_connection
=
False
...
...
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