diff --git a/mrdna/readers/test/libs b/mrdna/readers/test/libs
new file mode 120000
index 0000000000000000000000000000000000000000..d4bda9b46951e0c8c2007f84bbc447f93995502d
--- /dev/null
+++ b/mrdna/readers/test/libs
@@ -0,0 +1 @@
+../libs
\ No newline at end of file
diff --git a/mrdna/readers/test/s.csv b/mrdna/readers/test/s.csv
index 4bab8e1cbd0438888a345587cfc937468995a9a1..01ca2f5578a28f42e1351bc6ad4cbd0474314aee 100644
--- a/mrdna/readers/test/s.csv
+++ b/mrdna/readers/test/s.csv
@@ -1,416 +1,456 @@
-,0,vh,zid,fwd,stack_tuple,threeprime_tuple,x,y,z,r,seq,stack,threeprime,bp,orientation
-0,0,0,5,True,"(0, '6', True)","(0, '6', True)",0.0,22.5,17.0,[ 0. 22.5 17. ],-1,1,1,38,81.42857142857142
-1,1,0,6,True,"(0, '7', True)","(0, '7', True)",0.0,22.5,20.4,[ 0. 22.5 20.4],-1,2,2,39,115.71428571428572
-2,2,0,7,True,"(0, '8', True)","(0, '8', True)",0.0,22.5,23.8,[ 0. 22.5 23.8],-1,3,3,40,150.0
-3,3,0,8,True,"(0, '9', True)","(0, '9', True)",0.0,22.5,27.2,[ 0. 22.5 27.2],-1,4,4,41,184.28571428571428
-4,4,0,9,True,"(0, '10', True)","(0, '10', True)",0.0,22.5,30.599999999999998,[ 0. 22.5 30.6],-1,5,5,42,218.57142857142856
-5,5,0,10,True,"(0, '11', True)","(0, '11', True)",0.0,22.5,34.0,[ 0. 22.5 34. ],-1,6,6,43,252.85714285714283
-6,6,0,11,True,"(0, '12', True)","(0, '12', True)",0.0,22.5,37.4,[ 0. 22.5 37.4],-1,7,7,44,287.1428571428571
-7,7,0,12,True,"(0, '13', True)","(0, '13', True)",0.0,22.5,40.8,[ 0. 22.5 40.8],-1,8,8,45,321.42857142857144
-8,8,0,13,True,"(0, '14', True)","(0, '14', True)",0.0,22.5,44.199999999999996,[ 0. 22.5 44.2],-1,9,9,46,355.7142857142857
-9,9,0,14,True,"(0, '15', True)","(0, '15', True)",0.0,22.5,47.6,[ 0. 22.5 47.6],-1,10,10,47,390.0
-10,10,0,15,True,"(0, '16', True)","(0, '16', True)",0.0,22.5,51.0,[ 0. 22.5 51. ],-1,11,11,48,424.2857142857142
-11,11,0,16,True,"(0, '17', True)","(0, '17', True)",0.0,22.5,54.4,[ 0. 22.5 54.4],-1,12,12,49,458.57142857142856
-12,12,0,17,True,"(0, '18', True)","(0, '18', True)",0.0,22.5,57.8,[ 0. 22.5 57.8],-1,13,13,50,492.8571428571429
-13,13,0,18,True,"(0, '19', True)","(0, '19', True)",0.0,22.5,61.199999999999996,[ 0. 22.5 61.2],-1,14,14,51,527.1428571428571
-14,14,0,19,True,"(0, '20', True)","(0, '20', True)",0.0,22.5,64.6,[ 0. 22.5 64.6],-1,15,15,52,561.4285714285714
-15,15,0,20,True,"(0, '21', True)","(0, '21', True)",0.0,22.5,68.0,[ 0. 22.5 68. ],-1,16,16,53,595.7142857142857
-16,16,0,21,True,"(0, '22', True)","(0, '22', True)",0.0,22.5,71.39999999999999,[ 0. 22.5 71.4],-1,17,17,54,630.0
-17,17,0,22,True,"(0, '23', True)","(0, '23', True)",0.0,22.5,74.8,[ 0. 22.5 74.8],-1,18,18,55,664.2857142857142
-18,18,0,23,True,"(0, '24', True)","(0, '24', True)",0.0,22.5,78.2,[ 0. 22.5 78.2],-1,19,19,56,698.5714285714286
-19,19,0,24,True,"(0, '25', True)","(0, '25', True)",0.0,22.5,81.6,[ 0. 22.5 81.6],-1,20,20,57,732.8571428571429
-20,20,0,25,True,"(0, '26', True)","(0, '26', True)",0.0,22.5,85.0,[ 0. 22.5 85. ],-1,21,21,58,767.1428571428571
-21,21,0,26,True,"(0, '27', True)","(0, '27', True)",0.0,22.5,88.39999999999999,[ 0. 22.5 88.4],-1,22,22,59,801.4285714285714
-22,22,0,27,True,"(0, '28', True)","(0, '28', True)",0.0,22.5,91.8,[ 0. 22.5 91.8],-1,23,23,60,835.7142857142857
-23,23,0,28,True,"(0, '29', True)","(0, '29', True)",0.0,22.5,95.2,[ 0. 22.5 95.2],-1,24,24,61,870.0
-24,24,0,29,True,"(0, '30', True)","(0, '30', True)",0.0,22.5,98.6,[ 0. 22.5 98.6],-1,25,25,62,904.2857142857142
-25,25,0,30,True,"(0, '31', True)","(0, '31', True)",0.0,22.5,102.0,[ 0. 22.5 102. ],-1,26,26,63,938.5714285714284
-26,26,0,31,True,"(0, '32', True)","(0, '32', True)",0.0,22.5,105.39999999999999,[ 0. 22.5 105.4],-1,27,27,64,972.8571428571429
-27,27,0,32,True,"(0, '33', True)","(0, '33', True)",0.0,22.5,108.8,[ 0. 22.5 108.8],-1,28,28,65,1007.1428571428571
-28,28,0,33,True,"(0, '34', True)","(0, '34', True)",0.0,22.5,112.2,[ 0. 22.5 112.2],-1,29,29,66,1041.4285714285713
-29,29,0,34,True,"(0, '35', True)","(0, '35', True)",0.0,22.5,115.6,[ 0. 22.5 115.6],-1,30,30,67,1075.7142857142858
-30,30,0,35,True,"(0, '36', True)","(0, '36', True)",0.0,22.5,119.0,[ 0. 22.5 119. ],-1,31,31,68,1110.0
-31,31,0,36,True,-1,"(1, '36', False)",0.0,22.5,122.39999999999999,[ 0. 22.5 122.4],-1,-1,139,69,1144.2857142857142
-32,0,0,39,True,"(0, '40', True)","(0, '40', True)",0.0,22.5,132.6,[ 0. 22.5 132.6],-1,33,33,-1,1247.142857142857
-33,1,0,40,True,"(0, '41', True)","(0, '41', True)",0.0,22.5,136.0,[ 0. 22.5 136. ],-1,34,34,-1,1281.4285714285713
-34,2,0,41,True,-1,-1,0.0,22.5,139.4,[ 0. 22.5 139.4],-1,-1,-1,-1,1315.7142857142858
-35,0,0,2,False,-1,-1,0.0,22.5,6.8,[ 0. 22.5 6.8],-1,-1,-1,-1,-21.42857142857143
-36,1,0,3,False,"(0, '2', False)","(0, '2', False)",0.0,22.5,10.2,[ 0. 22.5 10.2],-1,35,35,-1,12.857142857142861
-37,2,0,4,False,"(0, '3', False)","(0, '3', False)",0.0,22.5,13.6,[ 0. 22.5 13.6],-1,36,36,-1,47.14285714285714
-38,3,0,5,False,"(0, '4', False)","(0, '4', False)",0.0,22.5,17.0,[ 0. 22.5 17. ],-1,37,37,0,81.42857142857142
-39,4,0,6,False,"(0, '5', False)","(0, '5', False)",0.0,22.5,20.4,[ 0. 22.5 20.4],-1,38,38,1,115.71428571428572
-40,5,0,7,False,"(0, '6', False)","(0, '6', False)",0.0,22.5,23.8,[ 0. 22.5 23.8],-1,39,39,2,150.0
-41,6,0,8,False,"(0, '7', False)","(0, '7', False)",0.0,22.5,27.2,[ 0. 22.5 27.2],-1,40,40,3,184.28571428571428
-42,7,0,9,False,"(0, '8', False)","(0, '8', False)",0.0,22.5,30.599999999999998,[ 0. 22.5 30.6],-1,41,41,4,218.57142857142856
-43,8,0,10,False,"(0, '9', False)","(0, '9', False)",0.0,22.5,34.0,[ 0. 22.5 34. ],-1,42,42,5,252.85714285714283
-44,9,0,11,False,"(0, '10', False)","(0, '10', False)",0.0,22.5,37.4,[ 0. 22.5 37.4],-1,43,43,6,287.1428571428571
-45,10,0,12,False,"(0, '11', False)","(0, '11', False)",0.0,22.5,40.8,[ 0. 22.5 40.8],-1,44,44,7,321.42857142857144
-46,11,0,13,False,"(0, '12', False)","(0, '12', False)",0.0,22.5,44.199999999999996,[ 0. 22.5 44.2],-1,45,45,8,355.7142857142857
-47,12,0,14,False,"(0, '13', False)","(0, '13', False)",0.0,22.5,47.6,[ 0. 22.5 47.6],-1,46,46,9,390.0
-48,13,0,15,False,"(0, '14', False)","(0, '14', False)",0.0,22.5,51.0,[ 0. 22.5 51. ],-1,47,47,10,424.2857142857142
-49,14,0,16,False,"(0, '15', False)","(0, '15', False)",0.0,22.5,54.4,[ 0. 22.5 54.4],-1,48,48,11,458.57142857142856
-50,15,0,17,False,"(0, '16', False)","(0, '16', False)",0.0,22.5,57.8,[ 0. 22.5 57.8],-1,49,49,12,492.8571428571429
-51,16,0,18,False,"(0, '17', False)","(0, '17', False)",0.0,22.5,61.199999999999996,[ 0. 22.5 61.2],-1,50,50,13,527.1428571428571
-52,17,0,19,False,"(0, '18', False)","(0, '18', False)",0.0,22.5,64.6,[ 0. 22.5 64.6],-1,51,51,14,561.4285714285714
-53,18,0,20,False,"(0, '19', False)","(0, '19', False)",0.0,22.5,68.0,[ 0. 22.5 68. ],-1,52,52,15,595.7142857142857
-54,0,0,21,False,-1,"(1, '21', True)",0.0,22.5,71.39999999999999,[ 0. 22.5 71.4],-1,-1,90,16,630.0
-55,1,0,22,False,"(0, '21', False)","(0, '21', False)",0.0,22.5,74.8,[ 0. 22.5 74.8],-1,54,54,17,664.2857142857142
-56,2,0,23,False,"(0, '22', False)","(0, '22', False)",0.0,22.5,78.2,[ 0. 22.5 78.2],-1,55,55,18,698.5714285714286
-57,0,0,24,False,-1,-1,0.0,22.5,81.6,[ 0. 22.5 81.6],-1,-1,-1,19,732.8571428571429
-58,1,0,25,False,"(0, '24', False)","(0, '24', False)",0.0,22.5,85.0,[ 0. 22.5 85. ],-1,57,57,20,767.1428571428571
-59,2,0,26,False,"(0, '25', False)","(0, '25', False)",0.0,22.5,88.39999999999999,[ 0. 22.5 88.4],-1,58,58,21,801.4285714285714
-60,3,0,27,False,"(0, '26', False)","(0, '26', False)",0.0,22.5,91.8,[ 0. 22.5 91.8],-1,59,59,22,835.7142857142857
-61,0,0,28,False,-1,"(5, '28', True)",0.0,22.5,95.2,[ 0. 22.5 95.2],-1,-1,368,23,870.0
-62,1,0,29,False,"(0, '28', False)","(0, '28', False)",0.0,22.5,98.6,[ 0. 22.5 98.6],-1,61,61,24,904.2857142857142
-63,2,0,30,False,"(0, '29', False)","(0, '29', False)",0.0,22.5,102.0,[ 0. 22.5 102. ],-1,62,62,25,938.5714285714284
-64,3,0,31,False,"(0, '30', False)","(0, '30', False)",0.0,22.5,105.39999999999999,[ 0. 22.5 105.4],-1,63,63,26,972.8571428571429
-65,4,0,32,False,"(0, '31', False)","(0, '31', False)",0.0,22.5,108.8,[ 0. 22.5 108.8],-1,64,64,27,1007.1428571428571
-66,5,0,33,False,"(0, '32', False)","(0, '32', False)",0.0,22.5,112.2,[ 0. 22.5 112.2],-1,65,65,28,1041.4285714285713
-67,6,0,34,False,"(0, '33', False)","(0, '33', False)",0.0,22.5,115.6,[ 0. 22.5 115.6],-1,66,66,29,1075.7142857142858
-68,7,0,35,False,"(0, '34', False)","(0, '34', False)",0.0,22.5,119.0,[ 0. 22.5 119. ],-1,67,67,30,1110.0
-69,8,0,36,False,"(0, '35', False)","(0, '35', False)",0.0,22.5,122.39999999999999,[ 0. 22.5 122.4],-1,68,68,31,1144.2857142857142
-70,9,0,37,False,"(0, '36', False)","(0, '36', False)",0.0,22.5,125.8,[ 0. 22.5 125.8],-1,69,69,-1,1178.5714285714284
-71,10,0,38,False,"(0, '37', False)","(0, '37', False)",0.0,22.5,129.2,[ 0. 22.5 129.2],-1,70,70,-1,1212.857142857143
-72,0,1,3,True,"(1, '4', True)","(1, '4', True)",-19.48557375,11.25,10.2,[-19.485573 11.25 10.2 ],-1,73,73,-1,12.857142857142861
-73,1,1,4,True,"(1, '5', True)","(1, '5', True)",-19.48557375,11.25,13.6,[-19.485573 11.25 13.6 ],-1,74,74,-1,47.14285714285714
-74,2,1,5,True,"(1, '6', True)","(1, '6', True)",-19.48557375,11.25,17.0,[-19.485573 11.25 17. ],-1,75,75,108,81.42857142857142
-75,3,1,6,True,"(1, '7', True)","(1, '7', True)",-19.48557375,11.25,20.4,[-19.485573 11.25 20.4 ],-1,76,76,109,115.71428571428572
-76,4,1,7,True,"(1, '8', True)","(1, '8', True)",-19.48557375,11.25,23.8,[-19.485573 11.25 23.8 ],-1,77,77,110,150.0
-77,5,1,8,True,"(1, '9', True)","(1, '9', True)",-19.48557375,11.25,27.2,[-19.485573 11.25 27.2 ],-1,78,78,111,184.28571428571428
-78,6,1,9,True,"(1, '10', True)","(1, '10', True)",-19.48557375,11.25,30.599999999999998,[-19.485573 11.25 30.6 ],-1,79,79,112,218.57142857142856
-79,7,1,10,True,"(1, '11', True)","(1, '11', True)",-19.48557375,11.25,34.0,[-19.485573 11.25 34. ],-1,80,80,113,252.85714285714283
-80,8,1,11,True,"(1, '12', True)","(1, '12', True)",-19.48557375,11.25,37.4,[-19.485573 11.25 37.4 ],-1,81,81,114,287.1428571428571
-81,9,1,12,True,"(1, '13', True)","(1, '13', True)",-19.48557375,11.25,40.8,[-19.485573 11.25 40.8 ],-1,82,82,115,321.42857142857144
-82,10,1,13,True,"(1, '14', True)","(1, '14', True)",-19.48557375,11.25,44.199999999999996,[-19.485573 11.25 44.2 ],-1,83,83,116,355.7142857142857
-83,11,1,14,True,"(1, '15', True)","(1, '15', True)",-19.48557375,11.25,47.6,[-19.485573 11.25 47.6 ],-1,84,84,117,390.0
-84,12,1,15,True,"(1, '16', True)","(1, '16', True)",-19.48557375,11.25,51.0,[-19.485573 11.25 51. ],-1,85,85,118,424.2857142857142
-85,13,1,16,True,"(1, '17', True)","(1, '17', True)",-19.48557375,11.25,54.4,[-19.485573 11.25 54.4 ],-1,86,86,119,458.57142857142856
-86,14,1,17,True,"(1, '18', True)","(1, '18', True)",-19.48557375,11.25,57.8,[-19.485573 11.25 57.8 ],-1,87,87,120,492.8571428571429
-87,15,1,18,True,"(1, '19', True)","(1, '19', True)",-19.48557375,11.25,61.199999999999996,[-19.485573 11.25 61.2 ],-1,88,88,121,527.1428571428571
-88,16,1,19,True,"(1, '20', True)","(1, '20', True)",-19.48557375,11.25,64.6,[-19.485573 11.25 64.6 ],-1,89,89,122,561.4285714285714
-89,17,1,20,True,-1,"(0, '20', False)",-19.48557375,11.25,68.0,[-19.485573 11.25 68. ],-1,-1,53,123,595.7142857142857
-90,0,1,21,True,"(1, '22', True)","(1, '22', True)",-19.48557375,11.25,71.39999999999999,[-19.485573 11.25 71.4 ],-1,91,91,124,630.0
-91,1,1,22,True,"(1, '23', True)","(1, '23', True)",-19.48557375,11.25,74.8,[-19.485573 11.25 74.8 ],-1,92,92,125,664.2857142857142
-92,2,1,23,True,"(1, '24', True)","(1, '24', True)",-19.48557375,11.25,78.2,[-19.485573 11.25 78.2 ],-1,93,93,126,698.5714285714286
-93,3,1,24,True,"(1, '25', True)","(1, '25', True)",-19.48557375,11.25,81.6,[-19.485573 11.25 81.6 ],-1,94,94,127,732.8571428571429
-94,4,1,25,True,"(1, '26', True)","(1, '26', True)",-19.48557375,11.25,85.0,[-19.485573 11.25 85. ],-1,95,95,128,767.1428571428571
-95,5,1,26,True,"(1, '27', True)","(1, '27', True)",-19.48557375,11.25,88.39999999999999,[-19.485573 11.25 88.4 ],-1,96,96,129,801.4285714285714
-96,6,1,27,True,"(1, '28', True)","(1, '28', True)",-19.48557375,11.25,91.8,[-19.485573 11.25 91.8 ],-1,97,97,130,835.7142857142857
-97,7,1,28,True,"(1, '29', True)","(1, '29', True)",-19.48557375,11.25,95.2,[-19.485573 11.25 95.2 ],-1,98,98,131,870.0
-98,8,1,29,True,"(1, '30', True)","(1, '30', True)",-19.48557375,11.25,98.6,[-19.485573 11.25 98.6 ],-1,99,99,132,904.2857142857142
-99,9,1,30,True,"(1, '31', True)","(1, '31', True)",-19.48557375,11.25,102.0,[-19.485573 11.25 102. ],-1,100,100,133,938.5714285714284
-100,10,1,31,True,"(1, '32', True)","(1, '32', True)",-19.48557375,11.25,105.39999999999999,[-19.485573 11.25 105.4 ],-1,101,101,134,972.8571428571429
-101,11,1,32,True,"(1, '33', True)","(1, '33', True)",-19.48557375,11.25,108.8,[-19.485573 11.25 108.8 ],-1,102,102,135,1007.1428571428571
-102,12,1,33,True,"(1, '34', True)","(1, '34', True)",-19.48557375,11.25,112.2,[-19.485573 11.25 112.2 ],-1,103,103,136,1041.4285714285713
-103,13,1,34,True,"(1, '35', True)","(1, '35', True)",-19.48557375,11.25,115.6,[-19.485573 11.25 115.6 ],-1,104,104,137,1075.7142857142858
-104,14,1,35,True,"(1, '36', True)","(1, '36', True)",-19.48557375,11.25,119.0,[-19.485573 11.25 119. ],-1,105,105,138,1110.0
-105,15,1,36,True,"(1, '37', True)","(1, '37', True)",-19.48557375,11.25,122.39999999999999,[-19.485573 11.25 122.4 ],-1,106,106,139,1144.2857142857142
-106,16,1,37,True,"(1, '38', True)","(1, '38', True)",-19.48557375,11.25,125.8,[-19.485573 11.25 125.8 ],-1,107,107,-1,1178.5714285714284
-107,17,1,38,True,-1,-1,-19.48557375,11.25,129.2,[-19.485573 11.25 129.2 ],-1,-1,-1,-1,1212.857142857143
-108,0,1,5,False,-1,"(0, '5', True)",-19.48557375,11.25,17.0,[-19.485573 11.25 17. ],-1,-1,0,74,81.42857142857142
-109,1,1,6,False,"(1, '5', False)","(1, '5', False)",-19.48557375,11.25,20.4,[-19.485573 11.25 20.4 ],-1,108,108,75,115.71428571428572
-110,2,1,7,False,"(1, '6', False)","(1, '6', False)",-19.48557375,11.25,23.8,[-19.485573 11.25 23.8 ],-1,109,109,76,150.0
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diff --git a/mrdna/readers/test/test.ipynb b/mrdna/readers/test/test.ipynb
index 60ee7259866dafeb7cbb1e125ae15ee3ba9fdaf0..e6aff5ff10d28e647d5337c78b99ddb632756bb4 100644
--- a/mrdna/readers/test/test.ipynb
+++ b/mrdna/readers/test/test.ipynb
@@ -17,6 +17,93 @@
"d=list(df[\"vstrands\"])"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "id": "5ebd0c89-5dd5-41a3-85e1-10b53cb34113",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
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+ " vertical-align: middle;\n",
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+ " .dataframe tbody tr th {\n",
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+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
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+ " <th></th>\n",
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+ " <th>5</th>\n",
+ " <td>6</td>\n",
+ " <td>1</td>\n",
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+ "source": [
+ "c=[1,2,3,4,5,6]\n",
+ "d=[2,3,4,5,6,1]\n",
+ "pd.DataFrame({\"c\":c,\"d\":d})"
+ ]
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{
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"execution_count": 2,
@@ -1955,7 +2042,7 @@
},
{
"cell_type": "code",
- "execution_count": 14,
+ "execution_count": 5,
"id": "5005611f",
"metadata": {},
"outputs": [
@@ -1965,7 +2052,7 @@
"210"
]
},
- "execution_count": 14,
+ "execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
@@ -1977,24 +2064,40 @@
},
{
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- "execution_count": 198,
+ "execution_count": 9,
+ "id": "b6643a5e-d63e-452d-99d0-0f0ad460bdf3",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "with open(\"test.virt2nuc\",\"rb\") as f:\n",
+ " df=pickle.load(f)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
"id": "83fc4ec6",
"metadata": {},
"outputs": [
{
- "ename": "TypeError",
- "evalue": "file must have 'read' and 'readline' attributes",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
- "Cell \u001b[0;32mIn[198], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[43mpickle\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mload\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mtest.virt2nuc\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\n",
- "\u001b[0;31mTypeError\u001b[0m: file must have 'read' and 'readline' attributes"
- ]
+ "data": {
+ "text/plain": [
+ "(<libs.cadnano_utils.vhelix_vbase_to_nucleotide at 0x7f9b1b65c820>,\n",
+ " {0: (12, 16),\n",
+ " 1: (12, 15),\n",
+ " 2: (13, 15),\n",
+ " 3: (13, 16),\n",
+ " 4: (13, 17),\n",
+ " 5: (12, 17)})"
+ ]
+ },
+ "execution_count": 10,
+ "metadata": {},
+ "output_type": "execute_result"
}
],
"source": [
- "df = pickle.load(\"test.virt2nuc\")"
+ "df"
]
},
{
@@ -2092,7 +2195,7 @@
},
{
"cell_type": "code",
- "execution_count": 187,
+ "execution_count": 198,
"id": "18132c9b",
"metadata": {},
"outputs": [
@@ -2306,99 +2409,5455 @@
" (3, 34)]]"
]
},
- "execution_count": 187,
+ "execution_count": 198,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "s1=decode_vh_vb(\"test.virt2nuc\")\n",
- "vh_vb,pattern=pd.read_pickle(\"test.virt2nuc\")\n",
+ "s1=decode_vh_vb(\"virt2nuc\")\n",
+ "vh_vb,pattern=pd.read_pickle(\"virt2nuc\")\n",
"list(find_segs(vh_vb._stap).values())"
]
},
{
"cell_type": "code",
- "execution_count": 142,
- "id": "087e2625",
+ "execution_count": 28,
+ "id": "dafaa4cf-47d9-4da3-8b63-1129c074c5ef",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "{0: (12, 16),\n",
+ " 1: (12, 15),\n",
+ " 2: (13, 15),\n",
+ " 3: (13, 16),\n",
+ " 4: (13, 17),\n",
+ " 5: (12, 17),\n",
+ " 6: (15, 5)}"
+ ]
+ },
+ "execution_count": 28,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "pattern"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "29e7336d-5ff3-4be1-bd47-585236ee7bb2",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 26,
+ "id": "75e15cf7-b1a3-4133-8bc4-3eaab5922b96",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
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+ " (3, 34): (13, [382])},\n",
+ " 'nuc_count': 0,\n",
+ " 'strand_count': 0}"
+ ]
+ },
+ "execution_count": 26,
+ "metadata": {},
+ "output_type": "execute_result"
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+ "vh_vb.__dict__"
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+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "list(vh_vb._scaf.values())"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 32,
+ "id": "704b72d9-4745-4818-83b5-934ca486e1bd",
+ "metadata": {},
+ "outputs": [
+ {
+ "ename": "KeyError",
+ "evalue": "0",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)",
+ "Cell \u001b[0;32mIn[32], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mvh_vb\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_scaf\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\n",
+ "\u001b[0;31mKeyError\u001b[0m: 0"
+ ]
+ }
+ ],
+ "source": [
+ "vh_vb._scaf[0]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 199,
+ "id": "5a920c32-cb2a-4a75-ac5a-d15fcff28aab",
"metadata": {},
"outputs": [],
"source": [
- "def find_segs(vir2nuc_scaf):\n",
- " oligos={}\n",
- " for i in range(len(vir2nuc_scaf)):\n",
- " oligo,ox_ind=list(vir2nuc_scaf.values())[i]\n",
- " if oligo not in oligos.keys():\n",
- " oligos[oligo]=[]\n",
- " oligos[oligo].append(list(vir2nuc_scaf.keys())[i])\n",
- " return oligos\n",
- "\n",
- "def decode_vh_vb(virt2nuc):\n",
- " vh_vb,pattern=pd.read_pickle(virt2nuc)\n",
- " vi={'row':0, 'col':0, 'num':0, 'scaf':dict(), 'stap':dict(), 'loop':[], 'skip':[], 'scafLoop':[],'stapLoop':[], 'stap_colors':[],\"scaf53\":True}\n",
- " vs=[] \n",
- " for i in range(len(pattern.keys())):\n",
- " vhi=vi.copy()\n",
- " vhi[\"row\"],vhi[\"col\"]=list(pattern.values())[i]\n",
- " vhi[\"num\"]=list(pattern.keys())[i]\n",
- " vs.append(vhi)\n",
- " vhelices=pd.DataFrame(vs)\n",
- " vhelices=vhelices.set_index('num')\n",
- " scafs=vh_vb._scaf\n",
- " staps=vh_vb._stap\n",
- " scaf_strands=find_segs(scafs)\n",
- " stap_strands=find_segs(staps)\n",
- " scaf_oligos=list(scaf_strands.keys())\n",
"\n",
- " \n",
- " return vhelices"
+ "def find_vh_vb_table(s,is_scaf):\n",
+ " L=[]\n",
+ " for i in list(s.keys()):\n",
+ " vh,zid=i\n",
+ " strand,indices=s[i]\n",
+ " if len(indices)==0:\n",
+ " continue\n",
+ " else:\n",
+ " if len(indices)==1:\n",
+ " zids=[str(zid)]\n",
+ " else:\n",
+ " zids=[str(zid)+\".\"+str(j) for j in range(len(indices))]\n",
+ " for index,z in zip(indices,zids):\n",
+ " L.append(pd.Series({\"index\":index,\"vh\":vh,\"zid\":z,\"strand\":strand,\"is_scaf\":bool(is_scaf)}))\n",
+ " return L\n",
+ "L1=find_vh_vb_table(vh_vb._scaf,1)\n",
+ "L2=find_vh_vb_table(vh_vb._stap,0)"
]
},
{
"cell_type": "code",
- "execution_count": 117,
- "id": "56387503",
+ "execution_count": 219,
+ "id": "8a6971b1-be0a-4546-90a7-918fa482f873",
"metadata": {},
"outputs": [],
"source": [
- "def find_base_map(oligo,i,vhx,scaf=True):\n",
- " vh0,vb0=oligo[i]\n",
- " vh1,vb1=oligo[i+1]\n",
- " if scaf==True:\n",
- " if vb0 not in vhx[\"scaf\"][vh0].keys():\n",
- " \n",
- " if vh0==vh1 and scaf==True:\n",
- " if vb0>vb1:\n",
- " vhx[vh0][\"scaf\"][vb0]=\n",
- " \n",
- "\n",
- " \n"
+ "df=pd.DataFrame(L1+L2)\n",
+ "pd.options.mode.chained_assignment = None # default='warn'"
]
},
{
"cell_type": "code",
- "execution_count": 116,
- "id": "c73234d5",
+ "execution_count": null,
+ "id": "1e8e7753-bb38-43a9-a33e-7882db3ace50",
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 255,
+ "id": "74ba42d3-aa69-4dd6-9c26-0023095b2923",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def get_virt2nuc(virt2nuc,top_data):\n",
+ " vh_vb,pattern=pd.read_pickle(virt2nuc)\n",
+ " L1=find_vh_vb_table(vh_vb._scaf,1)\n",
+ " L2=find_vh_vb_table(vh_vb._stap,0)\n",
+ " nt_prop=pd.DataFrame(L1+L2)\n",
+ " nt_prop.set_index(\"index\",inplace=True)\n",
+ " nt_prop.sort_index(inplace=True)\n",
+ " nt_prop[\"threeprime\"]=top_data[2]\n",
+ " nt_prop[\"seq\"]=top_data[1]\n",
+ " nt_prop[\"stack\"]=top_data[2]\n",
+ " for i in nt_prop.index:\n",
+ " if nt_prop.loc[i][\"threeprime\"] in nt_prop.index:\n",
+ " if nt_prop.loc[nt_prop.loc[i][\"threeprime\"]][\"vh\"]!=nt_prop.loc[i][\"vh\"]:\n",
+ " nt_prop[\"stack\"][i]=-1\n",
+ " bp_map=dict(zip(zip(nt_prop[\"vh\"],nt_prop[\"zid\"],nt_prop[\"is_scaf\"]),nt_prop.index))\n",
+ " bp=-np.ones(len(nt_prop.index),dtype=int)\n",
+ " counter=0\n",
+ " for i,j,k in zip(nt_prop[\"vh\"],nt_prop[\"zid\"],nt_prop[\"is_scaf\"]):\n",
+ " try:\n",
+ " bp[counter]=bp_map[(i,j,not(k))]\n",
+ " except:\n",
+ " pass\n",
+ " counter+=1\n",
+ " nt_prop[\"bp\"]=bp\n",
+ " return nt_prop"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 257,
+ "id": "74afbfe6-5fd3-4f41-8a41-c0aa56ddd1be",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "vh_vb,pattern=pd.read_pickle(\"virt2nuc\")\n",
+ "s=get_virt2nuc(\"virt2nuc\",top_data)\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 261,
+ "id": "9a115dac-e6cc-408c-9bc2-f33cf437f8c2",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "s.to_csv(\"s.csv\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 171,
+ "id": "170a2918-f113-475c-b0a3-edbf33153e33",
"metadata": {},
"outputs": [
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+ "execution_count": 171,
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+ " 373,\n",
+ " 372,\n",
+ " 371,\n",
+ " 370,\n",
+ " 369,\n",
+ " 368,\n",
+ " 336,\n",
+ " 335,\n",
+ " 334,\n",
+ " 333,\n",
+ " 332,\n",
+ " 331,\n",
+ " 330,\n",
+ " 292,\n",
+ " 291,\n",
+ " 290,\n",
+ " 289,\n",
+ " 288,\n",
+ " 287,\n",
+ " 286,\n",
+ " 285,\n",
+ " 284,\n",
+ " 283,\n",
+ " 282,\n",
+ " 281,\n",
+ " 280,\n",
+ " 279,\n",
+ " 278,\n",
+ " 277,\n",
+ " 276,\n",
+ " 275,\n",
+ " 274,\n",
+ " 273,\n",
+ " 272,\n",
+ " 271,\n",
+ " 270,\n",
+ " 269,\n",
+ " 268,\n",
+ " 267,\n",
+ " 309,\n",
+ " 308,\n",
+ " 307,\n",
+ " 306,\n",
+ " 305,\n",
+ " 304,\n",
+ " 303,\n",
+ " 302,\n",
+ " 301,\n",
+ " 300,\n",
+ " 299,\n",
+ " 298,\n",
+ " 297,\n",
+ " 296,\n",
+ " 295,\n",
+ " 26,\n",
+ " 25,\n",
+ " 24,\n",
+ " 23,\n",
+ " 22,\n",
+ " 21,\n",
+ " 20,\n",
+ " 19,\n",
+ " 18,\n",
+ " 17,\n",
+ " 16,\n",
+ " 15,\n",
+ " 14,\n",
+ " 13,\n",
+ " 12,\n",
+ " 11,\n",
+ " 420,\n",
+ " 419,\n",
+ " 418,\n",
+ " 417,\n",
+ " 416,\n",
+ " 415,\n",
+ " 414,\n",
+ " 413,\n",
+ " 412,\n",
+ " 411,\n",
+ " 410,\n",
+ " 409,\n",
+ " 408,\n",
+ " 407,\n",
+ " 396,\n",
+ " 395,\n",
+ " 394,\n",
+ " 393,\n",
+ " 392,\n",
+ " 391,\n",
+ " 390,\n",
+ " 355,\n",
+ " 354,\n",
+ " 353,\n",
+ " 352,\n",
+ " 351,\n",
+ " 350,\n",
+ " 349,\n",
+ " 348,\n",
+ " 347,\n",
+ " 346,\n",
+ " 345,\n",
+ " 344,\n",
+ " 343,\n",
+ " 342,\n",
+ " -1,\n",
+ " -1,\n",
+ " -1,\n",
+ " 197,\n",
+ " 196,\n",
+ " 195,\n",
+ " 194,\n",
+ " 193,\n",
+ " 192,\n",
+ " 191,\n",
+ " 190,\n",
+ " 189,\n",
+ " 188,\n",
+ " 187,\n",
+ " 186,\n",
+ " 185,\n",
+ " 184,\n",
+ " 183,\n",
+ " 182,\n",
+ " 181,\n",
+ " 180,\n",
+ " 179,\n",
+ " 178,\n",
+ " 177,\n",
+ " 176,\n",
+ " 175,\n",
+ " 174,\n",
+ " 173,\n",
+ " 172,\n",
+ " 128,\n",
+ " 127,\n",
+ " 212,\n",
+ " 211,\n",
+ " 210,\n",
+ " 209,\n",
+ " 208,\n",
+ " 207,\n",
+ " 206,\n",
+ " 205,\n",
+ " 204,\n",
+ " 203,\n",
+ " 202,\n",
+ " 201,\n",
+ " 200,\n",
+ " 199,\n",
+ " 198,\n",
+ " -1,\n",
+ " -1,\n",
+ " -1,\n",
+ " -1,\n",
+ " 144,\n",
+ " 143,\n",
+ " 142,\n",
+ " 141,\n",
+ " 140,\n",
+ " 139,\n",
+ " 138,\n",
+ " 137,\n",
+ " 136,\n",
+ " 135,\n",
+ " 134,\n",
+ " 133,\n",
+ " 132,\n",
+ " 131,\n",
+ " 130,\n",
+ " 129,\n",
+ " 171,\n",
+ " 170,\n",
+ " 169,\n",
+ " 168,\n",
+ " 167,\n",
+ " 166,\n",
+ " 165,\n",
+ " 60,\n",
+ " 59,\n",
+ " 58,\n",
+ " 57,\n",
+ " 56,\n",
+ " 263,\n",
+ " 262,\n",
+ " 261,\n",
+ " 260,\n",
+ " 259,\n",
+ " 258,\n",
+ " 257,\n",
+ " 256,\n",
+ " 255,\n",
+ " 254,\n",
+ " 253,\n",
+ " 252,\n",
+ " 251,\n",
+ " 250,\n",
+ " 72,\n",
+ " 71,\n",
+ " 70,\n",
+ " 69,\n",
+ " 68,\n",
+ " 67,\n",
+ " 66,\n",
+ " 65,\n",
+ " 64,\n",
+ " 63,\n",
+ " 62,\n",
+ " 61,\n",
+ " 164,\n",
+ " 163,\n",
+ " 162,\n",
+ " 161,\n",
+ " 160,\n",
+ " 159,\n",
+ " 158,\n",
+ " 157,\n",
+ " 156,\n",
+ " 155,\n",
+ " 154,\n",
+ " 153,\n",
+ " 152,\n",
+ " 151,\n",
+ " 150,\n",
+ " 149,\n",
+ " 148,\n",
+ " 147,\n",
+ " 146,\n",
+ " 145,\n",
+ " -1,\n",
+ " -1,\n",
+ " 249,\n",
+ " 248,\n",
+ " 247,\n",
+ " 246,\n",
+ " 245,\n",
+ " 244,\n",
+ " 243,\n",
+ " 96,\n",
+ " 95,\n",
+ " 94,\n",
+ " 93,\n",
+ " 92,\n",
+ " 101,\n",
+ " 100,\n",
+ " 99,\n",
+ " 98,\n",
+ " 97,\n",
+ " 242,\n",
+ " 241,\n",
+ " 240,\n",
+ " 239,\n",
+ " 238,\n",
+ " 237,\n",
+ " 236,\n",
+ " 235,\n",
+ " 234,\n",
+ " 233,\n",
+ " 232,\n",
+ " 231,\n",
+ " 230,\n",
+ " 229,\n",
+ " -1,\n",
+ " -1,\n",
+ " -1,\n",
+ " -1,\n",
+ " 112,\n",
+ " 111,\n",
+ " 110,\n",
+ " 109,\n",
+ " 108,\n",
+ " 107,\n",
+ " 106,\n",
+ " 105,\n",
+ " 104,\n",
+ " 103,\n",
+ " 102,\n",
+ " 91,\n",
+ " 90,\n",
+ " 89,\n",
+ " 88,\n",
+ " 87,\n",
+ " 86,\n",
+ " 85,\n",
+ " 84,\n",
+ " 83,\n",
+ " 82,\n",
+ " 81,\n",
+ " 80,\n",
+ " 79,\n",
+ " 78,\n",
+ " 77,\n",
+ " 76,\n",
+ " 75,\n",
+ " 74,\n",
+ " 73]"
+ ]
+ },
+ "execution_count": 176,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "vhzid=list(zip(dg[\"vh\"],dg[\"zid\"],dg[\"is_scaf\"]))\n",
+ "bp_list=dict(zip(vhzid,dg[\"index\"]))\n",
+ "bps =[]\n",
+ "for vh,zid,scaf in bp_list.keys():\n",
+ " try:\n",
+ " bps.append(bp_list[(vh,zid,not(scaf))])\n",
+ " except:\n",
+ " bps.append(-1)\n",
+ "bps "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 126,
+ "id": "9f960b0e-61d2-448e-bde9-a6595d733a11",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "top_data = np.loadtxt(\"test_insert.json.top\", skiprows=1,\n",
+ " unpack=True,\n",
+ " dtype=np.dtype('i4,U1,i4,i4')\n",
+ " )\n",
+ "dg=df.sort_index()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 128,
+ "id": "6df902fa-6979-403f-bef3-0afe2c4dac5f",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "[array([ 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4,\n",
+ " 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,\n",
+ " 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 6, 6, 6,\n",
+ " 6, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,\n",
+ " 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,\n",
+ " 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,\n",
+ " 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,\n",
+ " 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,\n",
+ " 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,\n",
+ " 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,\n",
+ " 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,\n",
+ " 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,\n",
+ " 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,\n",
+ " 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,\n",
+ " 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,\n",
+ " 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9,\n",
+ " 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9,\n",
+ " 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9,\n",
+ " 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,\n",
+ " 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11,\n",
+ " 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12,\n",
+ " 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12,\n",
+ " 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13,\n",
+ " 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,\n",
+ " 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14,\n",
+ " 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,\n",
+ " 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14], dtype=int32),\n",
+ " array(['C', 'C', 'G', 'G', 'T', 'C', 'G', 'G', 'G', 'C', 'A', 'A', 'A',\n",
+ " 'G', 'G', 'G', 'A', 'C', 'T', 'T', 'T', 'T', 'G', 'A', 'C', 'T',\n",
+ " 'G', 'T', 'G', 'C', 'C', 'C', 'C', 'C', 'A', 'A', 'A', 'A', 'G',\n",
+ " 'G', 'G', 'A', 'C', 'T', 'T', 'C', 'C', 'T', 'G', 'C', 'T', 'T',\n",
+ " 'G', 'A', 'C', 'A', 'T', 'A', 'G', 'T', 'G', 'C', 'G', 'G', 'C',\n",
+ " 'A', 'G', 'G', 'C', 'G', 'C', 'T', 'T', 'G', 'G', 'C', 'G', 'T',\n",
+ " 'G', 'A', 'A', 'C', 'C', 'T', 'C', 'G', 'C', 'A', 'T', 'G', 'G',\n",
+ " 'A', 'G', 'T', 'C', 'T', 'C', 'G', 'G', 'C', 'A', 'G', 'C', 'G',\n",
+ " 'T', 'G', 'T', 'C', 'C', 'G', 'C', 'G', 'T', 'C', 'C', 'C', 'T',\n",
+ " 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'G', 'C', 'A', 'C', 'C', 'C',\n",
+ " 'C', 'G', 'C', 'C', 'C', 'A', 'C', 'G', 'C', 'T', 'G', 'A', 'G',\n",
+ " 'G', 'C', 'G', 'A', 'A', 'C', 'C', 'A', 'A', 'A', 'G', 'T', 'A',\n",
+ " 'T', 'G', 'T', 'G', 'A', 'G', 'C', 'G', 'T', 'T', 'T', 'A', 'C',\n",
+ " 'A', 'C', 'T', 'T', 'A', 'T', 'C', 'A', 'C', 'T', 'C', 'T', 'A',\n",
+ " 'A', 'T', 'G', 'T', 'G', 'A', 'T', 'A', 'T', 'A', 'T', 'G', 'C',\n",
+ " 'C', 'C', 'G', 'T', 'C', 'C', 'A', 'G', 'A', 'C', 'G', 'A', 'T',\n",
+ " 'C', 'G', 'T', 'G', 'C', 'C', 'A', 'G', 'T', 'C', 'A', 'A', 'A',\n",
+ " 'A', 'G', 'T', 'C', 'C', 'C', 'T', 'T', 'T', 'T', 'A', 'T', 'C',\n",
+ " 'C', 'A', 'C', 'C', 'A', 'T', 'C', 'C', 'G', 'C', 'C', 'A', 'T',\n",
+ " 'A', 'C', 'C', 'C', 'C', 'A', 'A', 'A', 'C', 'T', 'A', 'G', 'G',\n",
+ " 'T', 'A', 'T', 'T', 'G', 'G', 'A', 'C', 'G', 'G', 'G', 'C', 'A',\n",
+ " 'T', 'A', 'T', 'A', 'T', 'C', 'A', 'C', 'A', 'T', 'T', 'A', 'G',\n",
+ " 'A', 'G', 'T', 'G', 'A', 'T', 'A', 'G', 'G', 'G', 'C', 'A', 'C',\n",
+ " 'G', 'A', 'T', 'C', 'G', 'T', 'C', 'T', 'G', 'G', 'A', 'T', 'T',\n",
+ " 'T', 'G', 'G', 'C', 'C', 'T', 'C', 'A', 'G', 'C', 'G', 'T', 'G',\n",
+ " 'G', 'G', 'C', 'G', 'G', 'A', 'G', 'T', 'G', 'T', 'A', 'A', 'C',\n",
+ " 'A', 'C', 'T', 'A', 'A', 'A', 'T', 'A', 'C', 'C', 'T', 'A', 'G',\n",
+ " 'T', 'T', 'T', 'G', 'G', 'A', 'A', 'G', 'C', 'G', 'C', 'C', 'T',\n",
+ " 'G', 'C', 'C', 'G', 'A', 'C', 'G', 'C', 'T', 'C', 'A', 'C', 'A',\n",
+ " 'T', 'A', 'C', 'T', 'T', 'T', 'G', 'G', 'T', 'T', 'C', 'A', 'G',\n",
+ " 'G', 'G', 'T', 'A', 'T', 'G', 'G', 'G', 'A', 'G', 'A', 'C', 'C',\n",
+ " 'T', 'G', 'C', 'C', 'C', 'G', 'G', 'A', 'T', 'G', 'G', 'T', 'G',\n",
+ " 'G', 'A', 'T', 'A', 'A', 'A', 'T', 'T', 'A', 'A', 'C', 'G', 'C',\n",
+ " 'G', 'G', 'A', 'C', 'A', 'C', 'G', 'T', 'C', 'C', 'A', 'T', 'G',\n",
+ " 'C', 'G', 'A', 'G', 'G', 'T', 'T', 'C', 'A', 'C', 'G', 'C', 'C'],\n",
+ " dtype='<U1'),\n",
+ " array([ -1, 0, 1, -1, 3, 4, -1, 6, 7, -1, 9, 10, 11,\n",
+ " 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,\n",
+ " 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,\n",
+ " 38, 39, 40, 41, -1, 43, 44, 45, 46, -1, 48, 49, 50,\n",
+ " -1, 52, 53, 54, -1, 56, 57, 58, 59, 60, 61, 62, 63,\n",
+ " 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,\n",
+ " 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89,\n",
+ " 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102,\n",
+ " 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115,\n",
+ " 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128,\n",
+ " 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141,\n",
+ " 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154,\n",
+ " 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167,\n",
+ " 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180,\n",
+ " 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193,\n",
+ " 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206,\n",
+ " 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219,\n",
+ " 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232,\n",
+ " 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245,\n",
+ " 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258,\n",
+ " 259, 260, 261, 262, -1, 264, 265, 266, 267, 268, 269, 270, 271,\n",
+ " 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284,\n",
+ " 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297,\n",
+ " 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310,\n",
+ " -1, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323,\n",
+ " 324, 325, 326, 327, 328, 329, 330, 331, -1, 333, 334, 335, 336,\n",
+ " 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349,\n",
+ " 350, 351, 352, 353, 354, -1, 356, 357, 358, 359, 360, 361, 362,\n",
+ " 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375,\n",
+ " 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388,\n",
+ " -1, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401,\n",
+ " 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414,\n",
+ " 415, 416, 417, 418, 419, 420, 421, -1, 423, 424, 425, 426, 427,\n",
+ " 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440,\n",
+ " 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453],\n",
+ " dtype=int32),\n",
+ " array([ 1, 2, -1, 4, 5, -1, 7, 8, -1, 10, 11, 12, 13,\n",
+ " 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,\n",
+ " 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39,\n",
+ " 40, 41, 42, -1, 44, 45, 46, 47, -1, 49, 50, 51, -1,\n",
+ " 53, 54, 55, -1, 57, 58, 59, 60, 61, 62, 63, 64, 65,\n",
+ " 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,\n",
+ " 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91,\n",
+ " 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104,\n",
+ " 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117,\n",
+ " 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130,\n",
+ " 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,\n",
+ " 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156,\n",
+ " 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169,\n",
+ " 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182,\n",
+ " 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195,\n",
+ " 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208,\n",
+ " 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221,\n",
+ " 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234,\n",
+ " 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247,\n",
+ " 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260,\n",
+ " 261, 262, 263, -1, 265, 266, 267, 268, 269, 270, 271, 272, 273,\n",
+ " 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286,\n",
+ " 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299,\n",
+ " 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, -1,\n",
+ " 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325,\n",
+ " 326, 327, 328, 329, 330, 331, 332, -1, 334, 335, 336, 337, 338,\n",
+ " 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351,\n",
+ " 352, 353, 354, 355, -1, 357, 358, 359, 360, 361, 362, 363, 364,\n",
+ " 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377,\n",
+ " 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, -1,\n",
+ " 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403,\n",
+ " 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416,\n",
+ " 417, 418, 419, 420, 421, 422, -1, 424, 425, 426, 427, 428, 429,\n",
+ " 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442,\n",
+ " 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, -1],\n",
+ " dtype=int32)]"
+ ]
+ },
+ "execution_count": 128,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "top_data"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 222,
+ "id": "9dbdf874-ed47-45bf-a70d-8c4928a5761b",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "dg[\"threeprime\"]=top_data[-1]\n",
+ "stacks=[]\n",
+ "dg[\"seq\"]=top_data[1]\n",
+ "dg[\"stack\"]=dg[\"threeprime\"]\n",
+ "for i in dg.index:\n",
+ " if dg.loc[i][\"threeprime\"] in dg.index:\n",
+ " if dg.loc[dg.loc[i][\"threeprime\"]][\"vh\"]!=dg.loc[i][\"vh\"]:\n",
+ " dg[\"stack\"][i]=-1\n"
+ ]
+ },
+ {
+ "cell_type": "code",
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+ "text/plain": [
+ " level_0 index vh zid strand is_scaf stack threeprime seq\n",
+ "0 0 0 0 41 0 True 1 1 C\n",
+ "1 1 1 0 40 0 True 2 2 C\n",
+ "2 2 2 0 39 0 True -1 -1 G\n",
+ "3 3 3 1 39 1 True 4 4 G\n",
+ "4 4 4 1 40 1 True 5 5 T\n",
+ ".. ... ... .. .. ... ... ... ... ..\n",
+ "450 450 450 4 35 13 False 451 451 A\n",
+ "451 451 451 4 36 13 False 452 452 C\n",
+ "452 452 452 4 37 13 False 453 453 G\n",
+ "453 453 453 4 38 13 False 454 454 C\n",
+ "454 454 454 4 39 13 False -1 -1 C\n",
+ "\n",
+ "[455 rows x 9 columns]"
+ ]
+ },
+ "execution_count": 179,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "dg"
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+ },
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+ "id": "9492a36d-ca4c-4859-833b-1f7831360c4e",
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+ " </tr>\n",
+ " <tr>\n",
+ " <th>451</th>\n",
+ " <td>451</td>\n",
+ " <td>451</td>\n",
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+ " <td>36</td>\n",
+ " <td>13</td>\n",
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+ " <td>76</td>\n",
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+ " <tr>\n",
+ " <th>453</th>\n",
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+ " </tr>\n",
+ " <tr>\n",
+ " <th>454</th>\n",
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+ " <td>454</td>\n",
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+ " <td>C</td>\n",
+ " <td>73</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "<p>455 rows × 10 columns</p>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " level_0 index vh zid strand is_scaf stack threeprime seq bp\n",
+ "0 0 0 0 41 0 True 1 1 C -1\n",
+ "1 1 1 0 40 0 True 2 2 C -1\n",
+ "2 2 2 0 39 0 True -1 -1 G -1\n",
+ "3 3 3 1 39 1 True 4 4 G -1\n",
+ "4 4 4 1 40 1 True 5 5 T -1\n",
+ ".. ... ... .. .. ... ... ... ... .. ..\n",
+ "450 450 450 4 35 13 False 451 451 A 77\n",
+ "451 451 451 4 36 13 False 452 452 C 76\n",
+ "452 452 452 4 37 13 False 453 453 G 75\n",
+ "453 453 453 4 38 13 False 454 454 C 74\n",
+ "454 454 454 4 39 13 False -1 -1 C 73\n",
+ "\n",
+ "[455 rows x 10 columns]"
+ ]
+ },
+ "execution_count": 196,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "bp_map=dict(zip(zip(dg[\"vh\"],dg[\"zid\"],dg[\"is_scaf\"]),dg[\"index\"]))\n",
+ "bp=-np.ones(len(dg.index),dtype=int)\n",
+ "counter=0\n",
+ "for i,j,k in zip(dg[\"vh\"],dg[\"zid\"],dg[\"is_scaf\"]):\n",
+ " try:\n",
+ " bp[counter]=bp_map[(i,j,not(k))]\n",
+ " except:\n",
+ " pass\n",
+ " counter+=1\n",
+ "dg[\"bp\"]=bp\n",
+ "dg"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 197,
+ "id": "319e2a8b-a24b-431e-80ec-6a21a8505ead",
+ "metadata": {},
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+ {
+ "data": {
+ "text/plain": [
+ "(level_0 450\n",
+ " index 450\n",
+ " vh 4\n",
+ " zid 35\n",
+ " strand 13\n",
+ " is_scaf False\n",
+ " stack 451\n",
+ " threeprime 451\n",
+ " seq A\n",
+ " bp 77\n",
+ " Name: 450, dtype: object,\n",
+ " level_0 77\n",
+ " index 77\n",
+ " vh 4\n",
+ " zid 35\n",
+ " strand 7\n",
+ " is_scaf True\n",
+ " stack 78\n",
+ " threeprime 78\n",
+ " seq T\n",
+ " bp 450\n",
+ " Name: 77, dtype: object)"
+ ]
+ },
+ "execution_count": 197,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "dg.loc[450],dg.loc[77]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 107,
+ "id": "d57bc82b-c233-4f0d-862e-47134101f43c",
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+ "source": [
+ "df[\"stack\"]=df.index[1:]+[-1]\n",
+ "df[\"threeprime\"]=df.index[1:]\n",
+ "\n",
+ "strands_map=df.groupby(['strand',\"vh\"]).groups\n",
+ "ind_map={}\n",
+ "for j in list(strands_map.keys()):\n",
+ " for l in strands_map[j]:\n",
+ " ind_map[l]=j\n",
+ "for i in list(df.index):\n",
+ " if df.loc[i]\n"
+ ]
+ },
+ {
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+ "execution_count": 99,
+ "id": "c88b4d35-0f58-47da-8687-e6a8433d363f",
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+ "execution_count": 99,
+ "metadata": {},
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+ "source": [
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+ "id": "eeea91ae-b631-454f-b66f-af580c7ece5c",
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+ ]
+ },
+ "execution_count": 84,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "strands=df.groupby(['strand']).groups\n",
+ "strands"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 88,
+ "id": "be4a60fe-444d-4772-80e8-b95591a079b3",
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+ ]
+ },
+ "execution_count": 88,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "threeprime=[]\n",
+ "for i in list(strands.values()):\n",
+ " m=list(i)\n",
+ " m.append(-1)\n",
+ " for j in range(1,len(m)):\n",
+ " threeprime.append(m[j])\n",
+ "threeprime"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 106,
+ "id": "dc9618ff-8016-480c-b704-31b2dc5f58a1",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
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+ "execution_count": 106,
+ "metadata": {},
+ "output_type": "execute_result"
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+ ],
+ "source": [
+ "stacks=[]\n",
+ "for i,j in zip(df.index,df[\"threeprime\"]):\n",
+ " try:\n",
+ " print(i,j)\n",
+ " if ind_map[i]==ind_map[j]:\n",
+ " stacks.append(j)\n",
+ " else:\n",
+ " stacks.append(-1)\n",
+ " except:\n",
+ " stacks.append(-1)\n",
+ "stacks"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 101,
+ "id": "64cb336b-9399-49ed-8a82-173a2b967a75",
+ "metadata": {},
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+ " 439: (13, 4),\n",
+ " 438: (13, 4),\n",
+ " 437: (13, 4),\n",
+ " 436: (13, 4)}"
+ ]
+ },
+ "execution_count": 101,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "strands2\n",
+ "ind_map={}\n",
+ "for j in list(strands2.keys()):\n",
+ " for l in strands2[j]:\n",
+ " ind_map[l]=j\n",
+ "ind_map\n",
+ " "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 97,
+ "id": "4a86b6be-8176-489c-a8a9-c31c62d04096",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
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+ " 437,\n",
+ " 436,\n",
+ " -1]"
+ ]
+ },
+ "execution_count": 97,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "strands2=df.groupby(['strand',\"vh\"]).groups\n",
+ "stacks=[]\n",
+ "for i in list(strands2.values()):\n",
+ " m=list(i)\n",
+ " m.append(-1)\n",
+ " for j in range(1,len(m)):\n",
+ " stacks.append(m[j])\n",
+ "stacks"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "id": "087e2625",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def find_segs(vir2nuc_scaf):\n",
+ " oligos={}\n",
+ " for i in range(len(vir2nuc_scaf)):\n",
+ " oligo,ox_ind=list(vir2nuc_scaf.values())[i]\n",
+ " if oligo not in oligos.keys():\n",
+ " oligos[oligo]=[]\n",
+ " oligos[oligo].append(list(vir2nuc_scaf.keys())[i])\n",
+ " return oligos\n",
+ "\n",
+ "def decode_vh_vb(virt2nuc):\n",
+ " vh_vb,pattern=pd.read_pickle(virt2nuc)\n",
+ " vi={'row':0, 'col':0, 'num':0, 'scaf':dict(), 'stap':dict(), 'loop':[], 'skip':[], 'scafLoop':[],'stapLoop':[], 'stap_colors':[],\"scaf53\":True}\n",
+ " vs=[] \n",
+ " for i in range(len(pattern.keys())):\n",
+ " vhi=vi.copy()\n",
+ " vhi[\"row\"],vhi[\"col\"]=list(pattern.values())[i]\n",
+ " vhi[\"num\"]=list(pattern.keys())[i]\n",
+ " vs.append(vhi)\n",
+ " vhelices=pd.DataFrame(vs)\n",
+ " vhelices=vhelices.set_index('num')\n",
+ " scafs=vh_vb._scaf\n",
+ " staps=vh_vb._stap\n",
+ " scaf_strands=find_segs(scafs)\n",
+ " stap_strands=find_segs(staps)\n",
+ " scaf_oligos=list(scaf_strands.keys())\n",
+ "\n",
+ " \n",
+ " return vhelices"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 117,
+ "id": "56387503",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def find_base_map(oligo,i,vhx,scaf=True):\n",
+ " vh0,vb0=oligo[i]\n",
+ " vh1,vb1=oligo[i+1]\n",
+ " if scaf==True:\n",
+ " if vb0 not in vhx[\"scaf\"][vh0].keys():\n",
+ " \n",
+ " if vh0==vh1 and scaf==True:\n",
+ " if vb0>vb1:\n",
+ " vhx[vh0][\"scaf\"][vb0]=\n",
+ " \n",
+ "\n",
+ " \n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "id": "c73234d5",
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "[(5, 22),\n",
+ " (5, 21),\n",
+ " (5, 20),\n",
+ " (5, 19),\n",
+ " (5, 18),\n",
+ " (5, 17),\n",
+ " (5, 16),\n",
+ " (5, 15),\n",
+ " (5, 14),\n",
+ " (5, 13),\n",
+ " (5, 12),\n",
+ " (5, 11),\n",
+ " (5, 10),\n",
+ " (5, 9),\n",
+ " (4, 9),\n",
" (4, 10),\n",
" (4, 11),\n",
" (4, 12),\n",
@@ -2574,7 +8033,7 @@
" (5, 23)]"
]
},
- "execution_count": 116,
+ "execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
diff --git a/mrdna/readers/test/test2.ipynb b/mrdna/readers/test/test2.ipynb
index ff33e4486a5b996733a0352dc849eefefb2b1935..2ebc69d8abad1e817d8e18950e7739adf839d85a 100644
--- a/mrdna/readers/test/test2.ipynb
+++ b/mrdna/readers/test/test2.ipynb
@@ -2,18 +2,10 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": 584,
"id": "9ea65628",
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "pip3 install termcolor\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"\n",
"from cadnano.document import Document\n",
@@ -27,7 +19,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 585,
"id": "1aaf81df-7464-4bd0-ace5-3b04e63815ac",
"metadata": {},
"outputs": [],
@@ -92,7 +84,7 @@
},
{
"cell_type": "code",
- "execution_count": 581,
+ "execution_count": 586,
"id": "c72e5d53-f082-4daa-8e36-6d74bfe8802b",
"metadata": {},
"outputs": [
@@ -110,7 +102,7 @@
},
{
"cell_type": "code",
- "execution_count": 574,
+ "execution_count": 587,
"id": "ff1c4a3c-9dde-4ea1-b360-f5d5d149b7d0",
"metadata": {},
"outputs": [],
@@ -170,7 +162,7 @@
},
{
"cell_type": "code",
- "execution_count": 577,
+ "execution_count": 612,
"id": "2356f6ba-8109-4ca1-8704-94f3c6a3bebd",
"metadata": {},
"outputs": [],
@@ -188,7 +180,7 @@
" nt_prop=pd.DataFrame(id_series)\n",
" nt_prop.reset_index(names=list(range(len(nt_prop.index))),inplace=True)\n",
" nt_prop[\"seq\"]=-1\n",
- " ind_tuple=[(nt_prop[\"vh\"][i],nt_prop[\"zid\"][i],nt_prop[\"fwd\"][i]) for i in nt_prop.index]\n",
+ " ind_tuple=list(zip(nt_prop[\"vh\"],nt_prop[\"zid\"],nt_prop[\"fwd\"]))\n",
" stacks=[]\n",
" for i in list(nt_prop[\"stack_tuple\"]):\n",
" if i ==-1:\n",
@@ -204,28 +196,1004 @@
" tprime.append(ind_tuple.index(i))\n",
" nt_prop[\"threeprime\"]=tprime\n",
" vhzid=list(zip(nt_prop[\"vh\"],nt_prop[\"zid\"]))\n",
- " nt_prop[\"bp\"]=-1\n",
" nt_prop[\"orientation\"]=[get_helix_angle(part, helix_id, int(float(indices))) for helix_id,indices in vhzid]\n",
" nt_prop=nt_prop.fillna(-1)\n",
- " for i in range(int(len(nt_prop.index)/2)):\n",
+ " counter=-1\n",
+ " bp=-np.ones(len(nt_prop.index),dtype=int)\n",
+ " bp_map=dict(zip(ind_tuple,nt_prop.index))\n",
+ " for i,j,k in ind_tuple:\n",
+ " counter+=1\n",
" try:\n",
- " bp1,bp2=(i,1+i+vhzid[i+1:].index(vhzid[i]))\n",
- " nt_prop[\"bp\"][bp1]=bp2\n",
- " nt_prop[\"bp\"][bp2]=bp1\n",
+ " bp[counter]=bp_map[(i,j,not(k))]\n",
" except:\n",
" pass\n",
+ " nt_prop[\"bp\"]=bp\n",
+ "\n",
" return nt_prop"
]
},
{
"cell_type": "code",
- "execution_count": 582,
+ "execution_count": 613,
"id": "d1e57e0e-efba-43c9-abdb-9fd7a7d0760b",
"metadata": {},
- "outputs": [],
+ "outputs": [
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+ "</table>\n",
+ "<p>415 rows × 15 columns</p>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " 0 vh zid fwd stack_tuple threeprime_tuple x y \\\n",
+ "0 0 0 5 True (0, 6, True) (0, 6, True) 0.000000 22.50 \n",
+ "1 1 0 6 True (0, 7, True) (0, 7, True) 0.000000 22.50 \n",
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+ "4 4 0 9 True (0, 10, True) (0, 10, True) 0.000000 22.50 \n",
+ ".. .. .. .. ... ... ... ... ... \n",
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+ "414 16 5 39 False (5, 38, False) (5, 38, False) 19.485574 11.25 \n",
+ "\n",
+ " z r seq stack threeprime orientation \\\n",
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+ "414 132.6 [19.485573, 11.25, 132.6] -1 413 413 1247.142857 \n",
+ "\n",
+ " bp \n",
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+ "4 42 \n",
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+ "\n",
+ "[415 rows x 15 columns]"
+ ]
+ },
+ "execution_count": 613,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "dg=gen_prop_table(part)\n",
+ "dg.to_csv(\"s.csv\")\n",
+ "dg"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 609,
+ "id": "c042b68c-6651-418e-b07c-dc3444afebdd",
+ "metadata": {},
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+ "\n",
+ "[415 rows x 390 columns]"
+ ]
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+ "execution_count": 609,
+ "metadata": {},
+ "output_type": "execute_result"
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+ "dg"
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+ "text/plain": [
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+ "0 0 0 5 True (0, 6, True) (0, 6, True) 0.000000 22.50 \n",
+ "1 1 0 6 True (0, 7, True) (0, 7, True) 0.000000 22.50 \n",
+ "2 2 0 7 True (0, 8, True) (0, 8, True) 0.000000 22.50 \n",
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+ "4 4 0 9 True (0, 10, True) (0, 10, True) 0.000000 22.50 \n",
+ ".. .. .. .. ... ... ... ... ... \n",
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+ "1 20.4 [0.0, 22.5, 20.4] -1 2 2 39 \n",
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+ "\n",
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+ "\n",
+ "[415 rows x 15 columns]"
+ ]
+ },
+ "execution_count": 604,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
"source": [
- "p=gen_prop_table(part)\n",
- "p.to_csv(\"s.csv\")"
+ "bp_map=dict(zip(zip(dg[\"vh\"],dg[\"id\"],dg[\"fwd\"]),dg.index))\n",
+ "bp=-np.ones(len(dg.index),dtype=int)\n",
+ "counter=0\n",
+ "for i,j,k in zip(dg[\"vh\"],dg[\"zid\"],dg[\"fwd\"]):\n",
+ " try:\n",
+ " bp[counter]=bp_map[(i,j,not(k))]\n",
+ " except:\n",
+ " pass\n",
+ " counter+=1\n",
+ "dg[\"bp\"]=bp\n",
+ "dg"
]
},
{
diff --git a/mrdna/readers/test/test_insert.json.oxdna b/mrdna/readers/test/test_insert.json.oxdna
new file mode 100644
index 0000000000000000000000000000000000000000..382e21729e7ec34e838bd44b73a24be3b3054329
--- /dev/null
+++ b/mrdna/readers/test/test_insert.json.oxdna
@@ -0,0 +1,458 @@
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