From ab0e3b721bdba8a06dc71559d31c91f9041fe4ba Mon Sep 17 00:00:00 2001
From: pinyili2 <pinyili2@illinois.edu>
Date: Wed, 21 Aug 2024 14:16:49 -0500
Subject: [PATCH] add
---
mrdna/readers/segmentmodel_from_cadnano.py | 5 +----
.../readers/segmentmodel_from_oxdna_pinyi.py | 21 ++++++++++++++-----
mrdna/readers/segmentmodel_from_scadnano.py | 8 +++++++
3 files changed, 25 insertions(+), 9 deletions(-)
diff --git a/mrdna/readers/segmentmodel_from_cadnano.py b/mrdna/readers/segmentmodel_from_cadnano.py
index 7c6c33c..a31a134 100644
--- a/mrdna/readers/segmentmodel_from_cadnano.py
+++ b/mrdna/readers/segmentmodel_from_cadnano.py
@@ -178,10 +178,7 @@ def gen_prop_table(part):
for i in not_stacked:
zid=int(nt_prop.loc[i]["zid"])
fwd=nt_prop.loc[i]["fwd"]
- if fwd == True:
- zid+=1
- else:
- zid-=1
+ zid+=fwd*2-1
try:
ind_tuple.index((nt_prop.loc[i]["vh"],str(zid),fwd))
nt_prop["stack_tuple"][i]=(nt_prop.loc[i]["vh"],str(zid),fwd)
diff --git a/mrdna/readers/segmentmodel_from_oxdna_pinyi.py b/mrdna/readers/segmentmodel_from_oxdna_pinyi.py
index b14e94f..9dcbbd1 100644
--- a/mrdna/readers/segmentmodel_from_oxdna_pinyi.py
+++ b/mrdna/readers/segmentmodel_from_oxdna_pinyi.py
@@ -103,15 +103,21 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
vh_bool=1-(nt_prop["vh"]%2)*2
is_scaf_bool=nt_prop["is_scaf"]*2-1
nt_prop["fwd"]=np.array((is_scaf_bool.T*vh_bool+1)/2,dtype=bool)
-
+ bp_map=dict(zip(zip(nt_prop["vh"],nt_prop["zid"],nt_prop["fwd"]),nt_prop.index))
+
for i in nt_prop.index:
if nt_prop.loc[i]["threeprime"] in nt_prop.index:
if nt_prop.loc[nt_prop.loc[i]["threeprime"]]["vh"]!=nt_prop.loc[i]["vh"]:
- nt_prop["stack"][i]=-1
- bp_map=dict(zip(zip(nt_prop["vh"],nt_prop["zid"],nt_prop["is_scaf"]),nt_prop.index))
+ vh=nt_prop.loc[i]["vh"]
+ zid=int(nt_prop.loc[i]["zid"])+int(nt_prop.loc[i]["fwd"])*2-1
+ if (vh,str(zid),nt_prop.loc[i]["fwd"]) in bp_map.keys():
+ nt_prop["stack"][i]=bp_map[ (vh,str(zid),nt_prop.loc[i]["fwd"])]
+ else:
+ nt_prop["stack"][i]=-1
+
bp=-np.ones(len(nt_prop.index),dtype=int)
counter=0
- for i,j,k in zip(nt_prop["vh"],nt_prop["zid"],nt_prop["is_scaf"]):
+ for i,j,k in zip(nt_prop["vh"],nt_prop["zid"],nt_prop["fwd"]):
try:
bp[counter]=bp_map[(i,j,not(k))]
except:
@@ -121,7 +127,12 @@ def mrdna_model_from_oxdna(coordinate_file, topology_file,virt2nuc=None,get_nt_p
non_stack_ind,=np.where(nt_prop["stack"]==-1)
for i in non_stack_ind:
- zid=nt_prop
+ zid=int(nt_prop.loc[i][zid])+int(nt_prop.loc[i]["fwd"])*2-1
+ try:
+ nt_prop["stack"][i]=bp_map[(nt_prop.loc[i]["vh"],str(zid),nt_prop.loc[i]["fwd"])]
+ except:
+ continue
+
return nt_prop
try:
nt_prop=get_virt2nuc(virt2nuc,top_data)
diff --git a/mrdna/readers/segmentmodel_from_scadnano.py b/mrdna/readers/segmentmodel_from_scadnano.py
index da2d4c4..863a61b 100644
--- a/mrdna/readers/segmentmodel_from_scadnano.py
+++ b/mrdna/readers/segmentmodel_from_scadnano.py
@@ -120,6 +120,14 @@ def gen_prop_table(fname):
except:
continue
nt_prop["bp"]=bp
+ non_stack_ind,=np.where(nt_prop["stack"]==-1)
+ for i in non_stack_ind:
+ zid=int(nt_prop.loc[i][zid])+int(nt_prop.loc[i]["fwd"])*2-1
+ try:
+ nt_prop["stack"][i]=bp_map[(nt_prop.loc[i]["vh"],str(zid),nt_prop.loc[i]["fwd"])]
+ except:
+ continue
+
nt_prop["r"]=list(np.array([nt_prop["x"],nt_prop["y"],nt_prop["z"]],dtype="<f4").T)
return nt_prop
--
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