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Klinische Genetica
prinia
Commits
8caf8042
Commit
8caf8042
authored
Aug 07, 2017
by
Sander Bollen
Browse files
primer3 object with subprocess
parent
ea30d85e
Changes
1
Hide whitespace changes
Inline
Side-by-side
prinia/primer3.py
0 → 100644
View file @
8caf8042
from
tempfile
import
NamedTemporaryFile
from
subprocess
import
check_call
try
:
from
StringIO
import
StringIO
except
ImportError
:
from
io
import
StringIO
class
Primer3
(
object
):
def
__init__
(
self
,
primer3_exe
,
template
,
target
,
excluded_region
,
opt_prim_length
=
25
,
opt_gc_perc
=
50
,
min_melting_t
=
58
,
max_melting_t
=
62
,
min_product_size
=
200
,
max_product_size
=
600
):
self
.
primer3_exe
=
primer3_exe
self
.
template
=
template
self
.
target
=
target
self
.
excluded_region
=
excluded_region
self
.
opt_prim_length
=
opt_prim_length
self
.
opt_gc_perc
=
opt_gc_perc
self
.
min_melting_t
=
min_melting_t
self
.
max_melting_t
=
max_melting_t
self
.
min_product_size
=
min_product_size
self
.
max_product_size
=
max_product_size
@
property
def
range
(
self
):
return
"{0}-{1}"
.
format
(
self
.
min_product_size
,
self
.
max_product_size
)
@
property
def
opt_size
(
self
):
return
int
(
self
.
min_product_size
+
(
float
((
self
.
max_product_size
-
self
.
min_product_size
))
/
2
)
)
def
create_config
(
self
,
handle
):
"""Create config for primer3."""
cfg_str
=
"SEQUENCE_ID=example
\n
"
\
"SEQUENCE_TEMPLATE={seq}
\n
"
\
"SEQUENCE_TARGET={tar}
\n
"
\
"SEQUENCE_EXCLUDED_REGION={exc}
\n
"
\
"PRIMER_TASK=pick_detection_primers
\n
"
\
"PRIMER_PICK_LEFT_PRIMER=1
\n
"
\
"PRIMER_PICK_INTERNAL_OLIGO=0
\n
"
\
"PRIMER_PICK_RIGHT_PRIMER=1
\n
"
\
"PRIMER_MIN_GC=20.0
\n
"
\
"PRIMER_INTERNAL_MIN_GC=20.0
\n
"
\
"PRIMER_OPT_GC_PERCENT={gc}
\n
"
\
"PRIMER_MAX_GC=80.0
\n
"
\
"PRIMER_INTERNAL_MAX_GC=80.0
\n
"
\
"PRIMER_WT_GC_PERCENT_LT=0.0
\n
"
\
"PRIMER_INTERNAL_WT_GC_PERCENT_LT=0.0
\n
"
\
"PRIMER_GC_CLAMP=0
\n
"
\
"PRIMER_MAX_END_GC=5
\n
"
\
"PRIMER_OPT_SIZE={size}
\n
"
\
"PRIMER_MIN_SIZE={isize}
\n
"
\
"PRIMER_MAX_SIZE={asize}
\n
"
\
"PRIMER_MAX_NS_ACCEPTED=0
\n
"
\
"PRIMER_PRODUCT_SIZE_RANGE={range}
\n
"
\
"PRIMER_PRODUCT_OPT_SIZE={osize}
\n
"
\
"PRIMER_PAIR_WT_PRODUCT_SIZE_GT=0.1
\n
"
\
"PRIMER_PAIR_WT_PRODUCT_SIZE_LT=0.1
\n
"
\
"P3_FILE_FLAG=1
\n
"
\
"SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
\n
"
\
"PRIMER_EXPLAIN_FLAG=1
\n
"
\
"PRIMER_MIN_TM={it}
\n
"
\
"PRIMER_MAX_TM={at}
\n
"
\
"PRIMER_NUM_RETURN=200"
.
format
(
seq
=
self
.
template
,
tar
=
self
.
target
,
exc
=
self
.
excluded_region
,
gc
=
self
.
opt_gc_perc
,
size
=
self
.
opt_prim_length
,
isize
=
self
.
opt_prim_length
-
5
,
asize
=
self
.
opt_prim_length
+
5
,
range
=
self
.
range
,
osize
=
self
.
opt_size
,
it
=
self
.
min_melting_t
,
at
=
self
.
max_melting_t
)
handle
.
write
(
cfg_str
)
def
run
(
self
):
cfg
=
NamedTemporaryFile
()
out
=
NamedTemporaryFile
()
self
.
create_config
(
cfg
)
args
=
[
self
.
primer3_exe
,
"-output"
,
out
.
name
,
cfg
.
name
]
_
=
check_call
(
args
=
args
)
retval
=
StringIO
()
with
open
(
out
.
name
)
as
handle
:
for
l
in
handle
:
retval
.
write
(
l
)
out
.
close
()
cfg
.
close
()
return
retval
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