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Klinische Genetica
prinia
Commits
63ef0435
Commit
63ef0435
authored
Oct 18, 2017
by
Sander Bollen
Browse files
reverse complement for reverse sequence
parent
e2996a03
Changes
1
Hide whitespace changes
Inline
Side-by-side
prinia/design.py
View file @
63ef0435
...
...
@@ -8,6 +8,7 @@ from subprocess import check_call, call
import
os
import
warnings
from
Bio.Seq
import
Seq
from
pyfaidx
import
Fasta
from
pysam
import
AlignmentFile
...
...
@@ -153,13 +154,18 @@ def _has_alternative_alignments(aligned_segment):
return
"XA"
in
[
x
[
0
]
for
x
in
tags
]
def
create_primer_from_pair
(
read1
,
read2
,
position
=
0
):
def
create_primer_from_pair
(
read1
,
read2
,
position
=
0
,
reverse_as_complement
=
True
):
"""Create primer from read pair"""
if
reverse_as_complement
:
seq
=
Seq
(
read2
.
query_sequence
)
reverse_seq
=
str
(
seq
.
reverse_complement
())
else
:
reverse_seq
=
read2
.
query_sequence
return
Primer
(
chromosome
=
read1
.
reference_name
,
position
=
position
,
left
=
read1
.
query_sequence
,
right
=
re
ad2
.
query_sequence
,
right
=
re
verse_seq
,
left_pos
=
read1
.
reference_start
,
right_pos
=
read2
.
reference_start
,
left_len
=
read1
.
query_length
,
...
...
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