Merge pull request #102 from Goosang-Yu/dev_goosang

✨ TwinPE design
Goosang-Yu · Oct 18, 2024 · b481623 · b481623
2 parents 4c30b93 + 76fabc0
commit b481623
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diff --git a/genet/__init__.py b/genet/__init__.py
@@ -7,7 +7,7 @@
 # How to release with 2FA accounts
 
 # [주의!] 먼저 아래의 version을 변경한다!!
-__version__ = '0.17.0'
+__version__ = '0.17.1'
 
 # hatch build
 # twine upload --username __token__ dist/*

diff --git a/genet/design/TwinPE.py b/genet/design/TwinPE.py
@@ -0,0 +1,40 @@
+from Bio.Seq import reverse_complement
+
+
+
+def twinPE(spacer_f:str, spacer_r:str, replace_seq:str, overlap:int=25, pbs_f:int=12, pbs_r:int=12) -> str:
+    """TwinPE에 필요한 pegRNA 2개의 RT-PBS를 디자인해주는 함수
+
+    Args:
+        spacer_f (str): pegRNA upper strand의 spacer
+        spacer_r (str): pegRNA bottom strand의 spacer
+        replace_seq (str): TwinPE로 replacement 하고 싶은 sequence
+        overlap (int, optional): TwinPE로 만들어지는 cDNA들의 overlap 길이. Defaults to 25.
+        pbs_f (int, optional): _description_. Defaults to 12.
+        pbs_r (int, optional): _description_. Defaults to 12.
+
+    Returns:
+        str: RT-PBS 2개 세트를 만들어 줌
+    """
+
+    if len(replace_seq) < overlap:
+        raise ValueError('The length of replace sequence must be longer than overlap length.')
+
+    spacer_f    = spacer_f.upper()
+    spacer_r    = spacer_r.upper()
+    replace_seq = replace_seq.upper()
+
+    pbs_f = reverse_complement(spacer_f[17-pbs_f:17])
+    pbs_r = reverse_complement(spacer_r[17-pbs_r:17])
+
+    RepSeq_center = int(len(replace_seq)/2)
+    half_overlap  = int(overlap/2)
+
+    cdna_f = reverse_complement(replace_seq[:RepSeq_center+half_overlap])
+    cdna_r = replace_seq[RepSeq_center-(overlap-half_overlap):]
+
+    rtpbs_1 = cdna_f + pbs_f
+    rtpbs_2 = cdna_r + pbs_r
+
+    return rtpbs_1, rtpbs_2
+
diff --git a/genet/design/__init__.py b/genet/design/__init__.py
@@ -1,3 +1,4 @@
 from .modules import *
 from genet.design.functional import *
+from genet.design.TwinPE import *
 from genet.design.DesignUtils import *