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Louis BECQUEY
/
RNANet
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Authored by
Louis BECQUEY
2020-05-29 14:44:05 +0200
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Commit
b910de9ec07aa8147681260d184f8783880c1e1a
b910de9e
1 parent
78e5248c
Supports mappings of multiple portions to one family
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Showing
2 changed files
with
16 additions
and
7 deletions
RNAnet.py
statistics.py
RNAnet.py
View file @
b910de9
...
...
@@ -540,6 +540,7 @@ class Chain:
self
.
seq_to_align
=
''
.
join
(
c_seq_to_align
)
self
.
seq
=
''
.
join
(
c_seq
)
class
Job
:
""" This class contains information about a task to run later.
...
...
@@ -574,6 +575,7 @@ class Job:
s
=
f
"{self.priority_}({self.nthreads}) [{self.comp_time}]
\t
{self.label:25}{self.func_.__name__}("
+
" "
.
join
([
str
(
a
)
for
a
in
self
.
args_
])
+
")"
return
s
class
Monitor
:
""" A job that simply watches the memory usage of another process.
...
...
@@ -1681,10 +1683,16 @@ def work_infer_mappings(update_only, allmappings, codelist):
for
rfam
in
families
:
# if a known mapping of this chain on this family exists, apply it
m
=
known_mappings
.
loc
[
(
known_mappings
.
pdb_id
+
"|1|"
+
known_mappings
.
chain
==
c
[:
4
]
.
lower
()
+
c
[
4
:])
&
(
known_mappings
[
'rfam_acc'
]
==
rfam
)
]
if
len
(
m
):
if
len
(
m
)
and
len
(
m
)
<
2
:
pdb_start
=
int
(
m
.
pdb_start
)
pdb_end
=
int
(
m
.
pdb_end
)
inferred
=
False
elif
len
(
m
):
# two different parts of the same chain are mapped to the same family... (ex: 6ek0-L5)
# ==> map the whole chain to that family, not the parts
pdb_start
=
int
(
m
.
pdb_start
.
min
())
pdb_end
=
int
(
m
.
pdb_end
.
max
())
inferred
=
False
else
:
# otherwise, use the inferred mapping
pdb_start
=
int
(
inferred_mappings
.
loc
[
(
inferred_mappings
[
'rfam_acc'
]
==
rfam
)
]
.
pdb_start
)
pdb_end
=
int
(
inferred_mappings
.
loc
[
(
inferred_mappings
[
'rfam_acc'
]
==
rfam
)
]
.
pdb_end
)
...
...
@@ -2114,7 +2122,7 @@ if __name__ == "__main__":
# At this point, the structure table is up to date
pp
.
build_chains
(
coeff_ncores
=
2
.0
)
pp
.
build_chains
(
coeff_ncores
=
1
.0
)
if
len
(
pp
.
to_retry
):
# Redownload and re-annotate
print
(
"> Retrying to annotate some structures which just failed."
,
flush
=
True
)
...
...
statistics.py
View file @
b910de9
...
...
@@ -87,6 +87,7 @@ def reproduce_wadley_results(show=False, carbon=4, sd_range=(1,4)):
kernel_c2
=
st
.
gaussian_kde
(
values_c2
)
f_c2
=
np
.
reshape
(
kernel_c2
(
positions
)
.
T
,
xx
.
shape
)
# Uncomment to save the data to an archive for later use without the need to recompute
np
.
savez
(
f
"data/wadley_kernel_{angle}.npz"
,
c3_endo_e
=
c3_endo_etas
,
c3_endo_t
=
c3_endo_thetas
,
...
...
@@ -516,16 +517,16 @@ if __name__ == "__main__":
mappings_list
[
k
]
=
[
x
[
0
]
for
x
in
sql_ask_database
(
conn
,
f
"SELECT chain_id from chain WHERE rfam_acc='{k}';"
)
]
conn
.
close
()
stats_pairs
()
#
stats_pairs()
# Define threads for the tasks
threads
=
[
th
.
Thread
(
target
=
reproduce_wadley_results
,
kwargs
=
{
'carbon'
:
1
}),
th
.
Thread
(
target
=
reproduce_wadley_results
,
kwargs
=
{
'carbon'
:
4
}),
th
.
Thread
(
target
=
stats_len
),
th
.
Thread
(
target
=
stats_freq
),
th
.
Thread
(
target
=
seq_idty
),
th
.
Thread
(
target
=
per_chain_stats
)
#
th.Thread(target=stats_len),
#
th.Thread(target=stats_freq),
#
th.Thread(target=seq_idty),
#
th.Thread(target=per_chain_stats)
]
# Start the threads
...
...
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