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Klinische Genetica
prinia
Commits
0aa9d54a
Commit
0aa9d54a
authored
Aug 09, 2017
by
Sander Bollen
Browse files
remove redundant code
parent
e451eef4
Changes
1
Hide whitespace changes
Inline
Side-by-side
prinia/design.py
View file @
0aa9d54a
...
...
@@ -289,18 +289,6 @@ def find_snps(primer, db_snp=None, field="AF"):
return
primer
def
_sanitize_p3
(
handle
):
# sanitize p3 output
# first line should always be removed:
_
=
next
(
handle
)
return
[
x
for
x
in
handle
if
"#"
not
in
x
.
decode
()]
def
_get_shortest
(
x
,
y
,
max_v
):
small
=
min
(
len
(
x
),
len
(
y
),
max_v
)
return
x
[:
small
],
y
[:
small
]
def
chop_region
(
region
,
size
):
"""
Chop a region in multiple regions with max size `size`
...
...
@@ -378,23 +366,3 @@ def get_primer_from_region(region, reference, product_size, n_prims,
if
len
(
primers
)
==
0
or
len
(
return_regions
)
==
0
:
raise
NoPrimersException
return
return_regions
,
primers
def
create_left_prim
(
primer
,
reference
):
primer_r_pos
=
primer
.
position
+
int
(
primer
.
right_pos
)
n_region
=
Region
(
start
=
primer_r_pos
-
len
(
primer
.
right
),
stop
=
primer_r_pos
,
chromosome
=
primer
.
chromosome
,
padding_left
=
0
,
padding_right
=
0
,
acc_nr
=
"NA"
,
other
=
"NA"
)
next_left_seq
=
get_sequence_fasta
(
n_region
,
reference
=
reference
,
padding
=
False
)
next_left_pos
=
primer_r_pos
-
len
(
primer
.
right
)
next_left_gc
=
calc_gc
(
next_left_seq
)
next_left
=
Primer
()
next_left
.
left
=
next_left_seq
next_left
.
left_gc
=
next_left_gc
next_left
.
left_pos
=
next_left_pos
next_left
.
left_len
=
len
(
next_left_seq
)
next_left
.
left_name
=
'.'
.
join
([
primer
.
chromosome
,
str
(
primer
.
position
)])
+
"_left"
next_left
.
chromosome
=
primer
.
chromosome
next_left
.
position
=
primer_r_pos
return
next_left
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