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vidjil
vidjil
Commits
c65f84e5
Commit
c65f84e5
authored
Jul 10, 2019
by
Mikaël Salson
Browse files
repseq_vdj.py: Field renaming for MiXCR
parent
50c032e4
Changes
1
Hide whitespace changes
Inline
Side-by-side
algo/tests/repseq_vdj.py
View file @
c65f84e5
...
...
@@ -155,16 +155,16 @@ class MiXCR_Result(Result):
return
None
def
populate
(
self
):
self
.
vdj
[
V
]
=
[
self
[
'
B
est
V h
it'
]]
if
self
[
'
B
est
D h
it'
]:
self
.
vdj
[
D
]
=
[
self
[
'
B
est
D h
it'
]]
self
.
vdj
[
J
]
=
[
self
[
'
B
est
J h
it'
]]
self
.
vdj
[
V
]
=
[
self
[
'
b
est
VH
it'
]]
if
self
[
'
b
est
DH
it'
]:
self
.
vdj
[
D
]
=
[
self
[
'
b
est
DH
it'
]]
self
.
vdj
[
J
]
=
[
self
[
'
b
est
JH
it'
]]
self
.
vdj
[
N1
]
=
self
[
'
N.
Seq
.
VDJunction'
]
self
.
vdj
[
N2
]
=
self
[
'
N.
Seq
.
DJJunction'
]
self
.
vdj
[
N
]
=
self
[
'
N.
Seq
.
VJJunction'
]
self
.
vdj
[
N1
]
=
self
[
'
n
SeqVDJunction'
]
self
.
vdj
[
N2
]
=
self
[
'
n
SeqDJJunction'
]
self
.
vdj
[
N
]
=
self
[
'
n
SeqVJJunction'
]
self
.
vdj
[
JUNCTION
]
=
self
[
'
AA.
Seq
.
CDR3'
]
self
.
vdj
[
JUNCTION
]
=
self
[
'
aa
SeqCDR3'
]
def
header_mixcr_results
(
ff_mixcr
):
...
...
@@ -177,7 +177,7 @@ def header_mixcr_results(ff_mixcr):
while
True
:
l
=
f
.
next
()
result
=
MiXCR_Result
(
l
)
yield
result
[
'
D
escr
iption
R1'
],
result
.
to_vdj
()
yield
result
[
'
d
escr
s
R1'
],
result
.
to_vdj
()
...
...
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