Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Klinische Genetica
prinia
Commits
c2c6fee7
Commit
c2c6fee7
authored
Jul 11, 2018
by
Sander Bollen
Browse files
dbsnp is not per se required
parent
86cbe6d0
Changes
2
Hide whitespace changes
Inline
Side-by-side
prinia/design.py
View file @
c2c6fee7
...
...
@@ -240,7 +240,7 @@ def create_primers_bwa(bam_handle, variant=None, region=None):
def
find_best_bwa
(
bam
,
variant
=
None
,
region
=
None
,
accept_snp
=
False
,
field
=
None
,
max_freq
=
None
,
dbsnp
=
None
):
primers
=
[]
for
primer
in
create_primers_bwa
(
bam
,
variant
=
variant
,
region
=
region
):
if
not
accept_snp
and
max_freq
is
not
None
:
if
not
accept_snp
and
max_freq
is
not
None
and
dbsnp
is
not
None
:
prim
=
find_snps
(
primer
,
dbsnp
,
field
)
if
prim
.
snp_freq
<=
max_freq
:
primers
.
append
(
prim
)
...
...
prinia/primerdesign.py
View file @
c2c6fee7
...
...
@@ -163,7 +163,7 @@ def main():
"(qualities will be sanger-encoded 40)"
)
parser
.
add_argument
(
'-R'
,
'--reference'
,
help
=
"Path to reference fasta file"
,
default
=
None
,
required
=
True
)
parser
.
add_argument
(
'--dbsnp'
,
help
=
"Path to DBSNP vcf"
,
default
=
None
,
required
=
Tru
e
)
parser
.
add_argument
(
'--dbsnp'
,
help
=
"Path to DBSNP vcf"
,
default
=
None
,
required
=
Fals
e
)
parser
.
add_argument
(
'--primer3'
,
help
=
"Path to primer3_core exe"
,
default
=
None
,
required
=
True
)
parser
.
add_argument
(
'--bwa'
,
help
=
"Path to BWA exe"
,
default
=
"bwa"
)
parser
.
add_argument
(
'--samtools'
,
help
=
"Path to samtools exe"
,
default
=
"samtools"
)
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment