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Mirrors
extractor
Commits
f37c14b8
Commit
f37c14b8
authored
Jun 21, 2016
by
jkvis
Browse files
Fixed an error in inserted prefix sequences in frame shifts
parent
365951f4
Changes
1
Hide whitespace changes
Inline
Side-by-side
extractor/describe.py
View file @
f37c14b8
...
...
@@ -358,20 +358,21 @@ def get_frames(flags):
def
describe_protein
(
s1
,
s2
,
codon_table
=
1
):
"""
"""
codons
=
util
.
codon_table_string
(
codon_table
)
codons
=
util
.
codon_table_string
(
codon_table
)
description
=
ProteinAllele
()
s1_swig
=
util
.
swig_str
(
s1
)
s2_swig
=
util
.
swig_str
(
s2
)
codons_swig
=
util
.
swig_str
(
codons
)
extracted
=
extractor
.
extract
(
s1_swig
[
0
],
s1_swig
[
1
],
s2_swig
[
0
],
s2_swig
[
1
],
extractor
.
TYPE_PROTEIN
,
codons_swig
[
0
])
variants
=
extracted
.
variants
#
for variant in variants:
#
print_var(variant)
#
print()
for
variant
in
variants
:
print_var
(
variant
)
print
()
index
=
0
while
index
<
len
(
variants
):
...
...
@@ -386,7 +387,7 @@ def describe_protein(s1, s2, codon_table=1):
while
(
index
<
len
(
variants
)
and
variants
[
index
].
type
&
extractor
.
FRAME_SHIFT
):
if
last_end
!=
variants
[
index
].
sample_start
:
if
last_end
<
variants
[
index
].
sample_start
:
seq_list
.
append
(
AISeq
(
s2
[
last_end
:
variants
[
index
].
sample_start
]))
...
...
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