From c3f9b21550f40bb4bcabfd197b65d7997ae37ca6 Mon Sep 17 00:00:00 2001
From: pinyili2 <pinyili2@illinois.edu>
Date: Fri, 2 Aug 2024 20:24:15 -0500
Subject: [PATCH] cad
---
mrdna/readers/cadnano_segments.py | 319 +++++++++++++++---------------
1 file changed, 159 insertions(+), 160 deletions(-)
diff --git a/mrdna/readers/cadnano_segments.py b/mrdna/readers/cadnano_segments.py
index 47cf148..b39bd2e 100644
--- a/mrdna/readers/cadnano_segments.py
+++ b/mrdna/readers/cadnano_segments.py
@@ -17,7 +17,166 @@ from ..model.dna_sequence import m13 as m13seq
## - helices that should be stacked across an empty region (crossovers from and end in the helix to another end in the helix)
## - circular constructs
+def combineRegionLists(loHi1,loHi2,intersect=False):
+
+ """Combines two lists of (lo,hi) pairs specifying integer
+ regions a single list of regions. """
+
+ ## Validate input
+ for l in (loHi1,loHi2):
+ ## Assert each region in lists is sorted
+ for pair in l:
+ assert(len(pair) == 2)
+ assert(pair[0] <= pair[1])
+
+ if len(loHi1) == 0:
+ if intersect:
+ return []
+ else:
+ return loHi2
+ if len(loHi2) == 0:
+ if intersect:
+ return []
+ else:
+ return loHi1
+
+ ## Break input into lists of compact regions
+ compactRegions1,compactRegions2 = [[],[]]
+ for compactRegions,loHi in zip(
+ [compactRegions1,compactRegions2],
+ [loHi1,loHi2]):
+ tmp = []
+ lastHi = loHi[0][0]-1
+ for lo,hi in loHi:
+ if lo-1 != lastHi:
+ compactRegions.append(tmp)
+ tmp = []
+ tmp.append((lo,hi))
+ lastHi = hi
+ if len(tmp) > 0:
+ compactRegions.append(tmp)
+
+ ## Build result
+ result = []
+ region = []
+ i,j = [0,0]
+ compactRegions1.append([[1e10]])
+ compactRegions2.append([[1e10]])
+ while i < len(compactRegions1)-1 or j < len(compactRegions2)-1:
+ cr1 = compactRegions1[i]
+ cr2 = compactRegions2[j]
+
+ ## initialize region
+ if len(region) == 0:
+ if cr1[0][0] <= cr2[0][0]:
+ region = cr1
+ i += 1
+ continue
+ else:
+ region = cr2
+ j += 1
+ continue
+
+ if region[-1][-1] >= cr1[0][0]:
+ region = combineCompactRegionLists(region, cr1, intersect=False)
+ i+=1
+ elif region[-1][-1] >= cr2[0][0]:
+ region = combineCompactRegionLists(region, cr2, intersect=False)
+ j+=1
+ else:
+ result.extend(region)
+ region = []
+
+ assert( len(region) > 0 )
+ result.extend(region)
+ result = sorted(result)
+
+ # print("loHi1:",loHi1)
+ # print("loHi2:",loHi2)
+ # print(result,"\n")
+
+ if intersect:
+ lo = max( [loHi1[0][0], loHi2[0][0]] )
+ hi = min( [loHi1[-1][1], loHi2[-1][1]] )
+ result = [r for r in result if r[0] >= lo and r[1] <= hi]
+
+ return result
+
+def combineCompactRegionLists(loHi1,loHi2,intersect=False):
+
+ """Combines two lists of (lo,hi) pairs specifying regions within a
+ compact integer set into a single list of regions.
+
+ examples:
+ loHi1 = [[0,4],[5,7]]
+ loHi2 = [[2,4],[5,9]]
+ out = [(0, 1), (2, 4), (5, 7), (8, 9)]
+
+ loHi1 = [[0,3],[5,7]]
+ loHi2 = [[2,4],[5,9]]
+ out = [(0, 1), (2, 3), (4, 4), (5, 7), (8, 9)]
+ """
+
+ ## Validate input
+ for l in (loHi1,loHi2):
+ ## Assert each region in lists is sorted
+ for pair in l:
+ assert(len(pair) == 2)
+ assert(pair[0] <= pair[1])
+ ## Assert lists are compact
+ for pair1,pair2 in zip(l[::2],l[1::2]):
+ assert(pair1[1]+1 == pair2[0])
+
+ if len(loHi1) == 0:
+ if intersect:
+ return []
+ else:
+ return loHi2
+ if len(loHi2) == 0:
+ if intersect:
+ return []
+ else:
+ return loHi1
+ ## Find the ends of the region
+ lo = min( [loHi1[0][0], loHi2[0][0]] )
+ hi = max( [loHi1[-1][1], loHi2[-1][1]] )
+
+ ## Make a list of indices where each region will be split
+ splitAfter = []
+ for l,h in loHi2:
+ if l != lo:
+ splitAfter.append(l-1)
+ if h != hi:
+ splitAfter.append(h)
+
+ for l,h in loHi1:
+ if l != lo:
+ splitAfter.append(l-1)
+ if h != hi:
+ splitAfter.append(h)
+ splitAfter = sorted(list(set(splitAfter)))
+
+ # print("splitAfter:",splitAfter)
+
+ split=[]
+ last = -2
+ for s in splitAfter:
+ split.append(s)
+ last = s
+
+ # print("split:",split)
+ returnList = [(i+1,j) if i != j else (i,j) for i,j in zip([lo-1]+split,split+[hi])]
+
+ if intersect:
+ lo = max( [loHi1[0][0], loHi2[0][0]] )
+ hi = min( [loHi1[-1][1], loHi2[-1][1]] )
+ returnList = [r for r in returnList if r[0] >= lo and r[1] <= hi]
+
+ # print("loHi1:",loHi1)
+ # print("loHi2:",loHi2)
+ # print(returnList,"\n")
+ return returnList
class cadnano_part(SegmentModel):
def __init__(self, part,
@@ -541,166 +700,6 @@ def read_model(json_data, sequence=None, fill_sequence='T', **kwargs):
# pynvml.nvmlShutdown()
# gpus = [0,1,2]
# print(gpus)
-def combineRegionLists(loHi1,loHi2,intersect=False):
-
- """Combines two lists of (lo,hi) pairs specifying integer
- regions a single list of regions. """
-
- ## Validate input
- for l in (loHi1,loHi2):
- ## Assert each region in lists is sorted
- for pair in l:
- assert(len(pair) == 2)
- assert(pair[0] <= pair[1])
-
- if len(loHi1) == 0:
- if intersect:
- return []
- else:
- return loHi2
- if len(loHi2) == 0:
- if intersect:
- return []
- else:
- return loHi1
-
- ## Break input into lists of compact regions
- compactRegions1,compactRegions2 = [[],[]]
- for compactRegions,loHi in zip(
- [compactRegions1,compactRegions2],
- [loHi1,loHi2]):
- tmp = []
- lastHi = loHi[0][0]-1
- for lo,hi in loHi:
- if lo-1 != lastHi:
- compactRegions.append(tmp)
- tmp = []
- tmp.append((lo,hi))
- lastHi = hi
- if len(tmp) > 0:
- compactRegions.append(tmp)
-
- ## Build result
- result = []
- region = []
- i,j = [0,0]
- compactRegions1.append([[1e10]])
- compactRegions2.append([[1e10]])
- while i < len(compactRegions1)-1 or j < len(compactRegions2)-1:
- cr1 = compactRegions1[i]
- cr2 = compactRegions2[j]
-
- ## initialize region
- if len(region) == 0:
- if cr1[0][0] <= cr2[0][0]:
- region = cr1
- i += 1
- continue
- else:
- region = cr2
- j += 1
- continue
-
- if region[-1][-1] >= cr1[0][0]:
- region = combineCompactRegionLists(region, cr1, intersect=False)
- i+=1
- elif region[-1][-1] >= cr2[0][0]:
- region = combineCompactRegionLists(region, cr2, intersect=False)
- j+=1
- else:
- result.extend(region)
- region = []
-
- assert( len(region) > 0 )
- result.extend(region)
- result = sorted(result)
-
- # print("loHi1:",loHi1)
- # print("loHi2:",loHi2)
- # print(result,"\n")
-
- if intersect:
- lo = max( [loHi1[0][0], loHi2[0][0]] )
- hi = min( [loHi1[-1][1], loHi2[-1][1]] )
- result = [r for r in result if r[0] >= lo and r[1] <= hi]
-
- return result
-
-def combineCompactRegionLists(loHi1,loHi2,intersect=False):
-
- """Combines two lists of (lo,hi) pairs specifying regions within a
- compact integer set into a single list of regions.
-
- examples:
- loHi1 = [[0,4],[5,7]]
- loHi2 = [[2,4],[5,9]]
- out = [(0, 1), (2, 4), (5, 7), (8, 9)]
-
- loHi1 = [[0,3],[5,7]]
- loHi2 = [[2,4],[5,9]]
- out = [(0, 1), (2, 3), (4, 4), (5, 7), (8, 9)]
- """
-
- ## Validate input
- for l in (loHi1,loHi2):
- ## Assert each region in lists is sorted
- for pair in l:
- assert(len(pair) == 2)
- assert(pair[0] <= pair[1])
- ## Assert lists are compact
- for pair1,pair2 in zip(l[::2],l[1::2]):
- assert(pair1[1]+1 == pair2[0])
-
- if len(loHi1) == 0:
- if intersect:
- return []
- else:
- return loHi2
- if len(loHi2) == 0:
- if intersect:
- return []
- else:
- return loHi1
-
- ## Find the ends of the region
- lo = min( [loHi1[0][0], loHi2[0][0]] )
- hi = max( [loHi1[-1][1], loHi2[-1][1]] )
-
- ## Make a list of indices where each region will be split
- splitAfter = []
- for l,h in loHi2:
- if l != lo:
- splitAfter.append(l-1)
- if h != hi:
- splitAfter.append(h)
-
- for l,h in loHi1:
- if l != lo:
- splitAfter.append(l-1)
- if h != hi:
- splitAfter.append(h)
- splitAfter = sorted(list(set(splitAfter)))
-
- # print("splitAfter:",splitAfter)
-
- split=[]
- last = -2
- for s in splitAfter:
- split.append(s)
- last = s
-
- # print("split:",split)
- returnList = [(i+1,j) if i != j else (i,j) for i,j in zip([lo-1]+split,split+[hi])]
-
- if intersect:
- lo = max( [loHi1[0][0], loHi2[0][0]] )
- hi = min( [loHi1[-1][1], loHi2[-1][1]] )
- returnList = [r for r in returnList if r[0] >= lo and r[1] <= hi]
-
- # print("loHi1:",loHi1)
- # print("loHi2:",loHi2)
- # print(returnList,"\n")
- return returnList
if __name__ == '__main__':
loHi1 = [[0,4],[5,7]]
--
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