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vidjil
vidjil
Commits
65444d0b
Commit
65444d0b
authored
Jul 10, 2019
by
Mikaël Salson
Browse files
repseq_vdj.py: Check key existence as all may not be filled all the time
parent
c65f84e5
Changes
1
Hide whitespace changes
Inline
Side-by-side
algo/tests/repseq_vdj.py
View file @
65444d0b
...
...
@@ -92,6 +92,9 @@ class Result(VDJ_Formatter):
self
.
populate
()
def
__contains__
(
self
,
key
):
return
key
in
self
.
d
def
__getitem__
(
self
,
key
):
return
self
.
d
[
key
]
...
...
@@ -160,11 +163,15 @@ class MiXCR_Result(Result):
self
.
vdj
[
D
]
=
[
self
[
'bestDHit'
]]
self
.
vdj
[
J
]
=
[
self
[
'bestJHit'
]]
self
.
vdj
[
N1
]
=
self
[
'nSeqVDJunction'
]
self
.
vdj
[
N2
]
=
self
[
'nSeqDJJunction'
]
self
.
vdj
[
N
]
=
self
[
'nSeqVJJunction'
]
if
'nSeqVDJunction'
in
self
:
self
.
vdj
[
N1
]
=
self
[
'nSeqVDJunction'
]
if
'nSeqDJJunction'
in
self
:
self
.
vdj
[
N2
]
=
self
[
'nSeqDJJunction'
]
if
'nSeqVJJunction'
in
self
:
self
.
vdj
[
N
]
=
self
[
'nSeqVJJunction'
]
self
.
vdj
[
JUNCTION
]
=
self
[
'aaSeqCDR3'
]
if
'aaSeqCDR3'
in
self
:
self
.
vdj
[
JUNCTION
]
=
self
[
'aaSeqCDR3'
]
def
header_mixcr_results
(
ff_mixcr
):
...
...
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