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Louis BECQUEY
/
RNANet
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Authored by
Louis BECQUEY
2020-07-23 16:37:44 +0200
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Commit
18394e1c7f6bc5342c88899327ac8ad05051b551
18394e1c
1 parent
5af4d125
debugged doublon checking in MSAs
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2 additions
and
3 deletions
RNAnet.py
RNAnet.py
View file @
18394e1
...
...
@@ -557,7 +557,6 @@ class Chain:
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?);"""
,
many
=
True
,
data
=
list
(
df
.
to_records
(
index
=
False
)),
warn_every
=
10
)
def
remap
(
self
,
columns_to_save
,
s_seq
):
"""Maps the object's sequence to its version in a MSA, to compute nucleotide frequencies at every position.
...
...
@@ -2035,10 +2034,10 @@ def work_realign(rfam_acc):
notify
(
"Aligned new sequences together"
)
# Detect doublons and remove them
existing_stk
=
AlignIO
.
parse
(
existing_ali_path
,
"stockholm"
)
existing_stk
=
AlignIO
.
read
(
existing_ali_path
,
"stockholm"
)
existing_ids
=
[
r
.
id
for
r
in
existing_stk
]
del
existing_stk
new_stk
=
AlignIO
.
parse
(
new_ali_path
,
"stk"
)
new_stk
=
AlignIO
.
read
(
new_ali_path
,
"stk"
)
new_ids
=
[
r
.
id
for
r
in
new_stk
]
del
new_stk
doublons
=
[
i
for
i
in
existing_ids
if
i
in
new_ids
]
...
...
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