From ce3875b76e4d14ad85c52405bb2bab7aab40890b Mon Sep 17 00:00:00 2001
From: pinyili2 <pinyili2@illinois.edu>
Date: Tue, 13 Aug 2024 22:50:39 -0500
Subject: [PATCH] add
---
mrdna/readers/segmentmodel_from_cadnano.py | 18 ++++--------------
1 file changed, 4 insertions(+), 14 deletions(-)
diff --git a/mrdna/readers/segmentmodel_from_cadnano.py b/mrdna/readers/segmentmodel_from_cadnano.py
index 610be17..6cb46ea 100644
--- a/mrdna/readers/segmentmodel_from_cadnano.py
+++ b/mrdna/readers/segmentmodel_from_cadnano.py
@@ -158,7 +158,7 @@ def gen_id_series(strand,part):
return [pd.Series(df.loc[i]) for i in df.index]
-def gen_prop_table(part,seq_file=None,fill_seq="T"):
+def gen_prop_table(part):
strand_set=[]
for i in part.getidNums():
fwd,rev=part.getStrandSets(i)
@@ -197,16 +197,6 @@ def gen_prop_table(part,seq_file=None,fill_seq="T"):
nt_prop["bp"][bp2]=bp1
except:
pass
- if seq_file is not None:
- #under construction
- seq=open(seq_file,"r")
- for seqline in seq:
- try:
- int(seqline[0])
- except:
- continue
-
-
return nt_prop
@@ -214,9 +204,9 @@ def mrdna_model_from_cadnano(json_file,seq=None,**model_parameters):
json_data=read_json_file(json_file)
part,decoder=cadnano_parts(json_data)
if decoder==2:
- nt_prop=gen_prop_table_cad2(json_data,part)
+ nt_prop=gen_prop_table(part)
elif decoder==3:
- nt_prop=gen_prop_table_cad3(json_data,part)
+ nt_prop=gen_prop_table(part)
if seq is None:
if nt_prop["seq"][0]==-1:
@@ -229,5 +219,5 @@ def mrdna_model_from_cadnano(json_file,seq=None,**model_parameters):
three_prime=np.array((list(nt_prop["threeprime"])))
stack=np.array((list(nt_prop["stack"])))
orientation=np.array(list(nt_prop["orientation"]))
- model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation=None, **model_parameters )
+ model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )
return model
--
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