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doublergreerdoublergreer
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get backbone and single part checking
1 parent a1c4e20 commit c8811a2

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Lines changed: 249 additions & 83 deletions

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‎notebooks/build_compiler_test.ipynb‎

Lines changed: 155 additions & 71 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
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"cells": [
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{
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"cell_type": "code",
5-
"execution_count": null,
5+
"execution_count": 28,
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"id": "87bdb42e",
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"metadata": {},
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"outputs": [],
@@ -22,7 +22,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": 29,
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"id": "66608e09",
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"metadata": {},
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"outputs": [],
@@ -39,7 +39,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 30,
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"id": "53a1bc5c",
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"metadata": {},
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"outputs": [],
@@ -206,12 +206,12 @@
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": 31,
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"id": "90648527",
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"metadata": {},
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"outputs": [],
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"source": [
214-
"auth = \"d83bd9af-be31-47ca-ae1a-dcb34207daf6\"\n",
214+
"auth = \"6aed3476-ac43-412f-8ee7-9d066024e661\"\n",
215215
"buildcompiler = BuildCompiler(None, \"https://synbiohub.org\", auth)\n",
216216
"\n",
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"buildcompiler.index_collections(\n",
@@ -223,7 +223,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": 32,
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"id": "99d093a8",
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"metadata": {},
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"outputs": [
@@ -232,28 +232,28 @@
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"output_type": "stream",
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"text": [
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"Plasmids: [Plasmid:\n",
235-
" Name: pB0032_BC_B_C\n",
236-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0032_BC/1\n",
235+
" Name: pB0034_BC_B_C\n",
236+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0034_BC/1\n",
237237
" Strain: None\n",
238238
" Fusion Sites: ['B', 'C'] Antibiotic Resistance: Ampicillin\n",
239239
", Plasmid:\n",
240-
" Name: pE1010_CD_C_D\n",
241-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pE1010_CD/1\n",
240+
" Name: pJ23106_AB_A_B\n",
241+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23106_AB/1\n",
242242
" Strain: None\n",
243-
" Fusion Sites: ['C', 'D'] Antibiotic Resistance: Ampicillin\n",
243+
" Fusion Sites: ['A', 'B'] Antibiotic Resistance: Ampicillin\n",
244244
", Plasmid:\n",
245-
" Name: pJ23106_GB_B_G\n",
246-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23106_GB/1\n",
245+
" Name: pB0015_DF_D_F\n",
246+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0015_DF/1\n",
247247
" Strain: None\n",
248-
" Fusion Sites: ['B', 'G'] Antibiotic Resistance: Ampicillin\n",
248+
" Fusion Sites: ['D', 'F'] Antibiotic Resistance: Ampicillin\n",
249249
", Plasmid:\n",
250-
" Name: pB0033_BC_B_C\n",
251-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0033_BC/1\n",
250+
" Name: pB0032_BC_B_C\n",
251+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0032_BC/1\n",
252252
" Strain: None\n",
253253
" Fusion Sites: ['B', 'C'] Antibiotic Resistance: Ampicillin\n",
254254
", Plasmid:\n",
255-
" Name: pJ23116_GB_B_G\n",
256-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23116_GB/1\n",
255+
" Name: pJ23106_GB_B_G\n",
256+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23106_GB/1\n",
257257
" Strain: None\n",
258258
" Fusion Sites: ['B', 'G'] Antibiotic Resistance: Ampicillin\n",
259259
", Plasmid:\n",
@@ -262,25 +262,30 @@
262262
" Strain: None\n",
263263
" Fusion Sites: ['B', 'F'] Antibiotic Resistance: Ampicillin\n",
264264
", Plasmid:\n",
265-
" Name: pB0015_DE_D_E\n",
266-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0015_DE/1\n",
265+
" Name: pJ23100_AB_A_B\n",
266+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23100_AB/1\n",
267267
" Strain: None\n",
268-
" Fusion Sites: ['D', 'E'] Antibiotic Resistance: Ampicillin\n",
268+
" Fusion Sites: ['A', 'B'] Antibiotic Resistance: Ampicillin\n",
269+
", Plasmid:\n",
270+
" Name: pE1010_CD_C_D\n",
271+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pE1010_CD/1\n",
272+
" Strain: None\n",
273+
" Fusion Sites: ['C', 'D'] Antibiotic Resistance: Ampicillin\n",
269274
", Plasmid:\n",
270275
" Name: pB0015_DG_D_G\n",
271276
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0015_DG/1\n",
272277
" Strain: None\n",
273278
" Fusion Sites: ['D', 'G'] Antibiotic Resistance: Ampicillin\n",
274279
", Plasmid:\n",
275-
" Name: pJ23100_FB_B_F\n",
276-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23100_FB/1\n",
280+
" Name: pB0033_BC_B_C\n",
281+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0033_BC/1\n",
277282
" Strain: None\n",
278-
" Fusion Sites: ['B', 'F'] Antibiotic Resistance: Ampicillin\n",
283+
" Fusion Sites: ['B', 'C'] Antibiotic Resistance: Ampicillin\n",
279284
", Plasmid:\n",
280-
" Name: pJ23100_GB_B_G\n",
281-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23100_GB/1\n",
285+
" Name: pJ23106_EB_B_E\n",
286+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23106_EB/1\n",
282287
" Strain: None\n",
283-
" Fusion Sites: ['B', 'G'] Antibiotic Resistance: Ampicillin\n",
288+
" Fusion Sites: ['B', 'E'] Antibiotic Resistance: Ampicillin\n",
284289
", Plasmid:\n",
285290
" Name: pJ23116_EB_B_E\n",
286291
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23116_EB/1\n",
@@ -292,67 +297,52 @@
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" Strain: None\n",
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" Fusion Sites: ['B', 'E'] Antibiotic Resistance: Ampicillin\n",
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", Plasmid:\n",
295-
" Name: pJ23106_AB_A_B\n",
296-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23106_AB/1\n",
300+
" Name: pJ23100_GB_B_G\n",
301+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23100_GB/1\n",
297302
" Strain: None\n",
298-
" Fusion Sites: ['A', 'B'] Antibiotic Resistance: Ampicillin\n",
303+
" Fusion Sites: ['B', 'G'] Antibiotic Resistance: Ampicillin\n",
299304
", Plasmid:\n",
300305
" Name: pE0040_CD_C_D\n",
301306
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pE0040_CD/1\n",
302307
" Strain: None\n",
303308
" Fusion Sites: ['C', 'D'] Antibiotic Resistance: Ampicillin\n",
304309
", Plasmid:\n",
305-
" Name: pJ23106_EB_B_E\n",
306-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23106_EB/1\n",
310+
" Name: pJ23116_AB_A_B\n",
311+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23116_AB/1\n",
307312
" Strain: None\n",
308-
" Fusion Sites: ['B', 'E'] Antibiotic Resistance: Ampicillin\n",
313+
" Fusion Sites: ['A', 'B'] Antibiotic Resistance: Ampicillin\n",
314+
", Plasmid:\n",
315+
" Name: pJ23116_FB_B_F\n",
316+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23116_FB/1\n",
317+
" Strain: None\n",
318+
" Fusion Sites: ['B', 'F'] Antibiotic Resistance: Ampicillin\n",
309319
", Plasmid:\n",
310320
" Name: pE0030_CD_C_D\n",
311321
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pE0030_CD/1\n",
312322
" Strain: None\n",
313323
" Fusion Sites: ['C', 'D'] Antibiotic Resistance: Ampicillin\n",
314324
", Plasmid:\n",
315-
" Name: pB0034_BC_B_C\n",
316-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0034_BC/1\n",
317-
" Strain: None\n",
318-
" Fusion Sites: ['B', 'C'] Antibiotic Resistance: Ampicillin\n",
319-
", Plasmid:\n",
320-
" Name: pJ23100_AB_A_B\n",
321-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23100_AB/1\n",
322-
" Strain: None\n",
323-
" Fusion Sites: ['A', 'B'] Antibiotic Resistance: Ampicillin\n",
324-
", Plasmid:\n",
325325
" Name: pB0015_DH_D_H\n",
326326
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0015_DH/1\n",
327327
" Strain: None\n",
328328
" Fusion Sites: ['D', 'H'] Antibiotic Resistance: Ampicillin\n",
329329
", Plasmid:\n",
330-
" Name: pJ23116_FB_B_F\n",
331-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23116_FB/1\n",
330+
" Name: pB0015_DE_D_E\n",
331+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0015_DE/1\n",
332332
" Strain: None\n",
333-
" Fusion Sites: ['B', 'F'] Antibiotic Resistance: Ampicillin\n",
333+
" Fusion Sites: ['D', 'E'] Antibiotic Resistance: Ampicillin\n",
334334
", Plasmid:\n",
335-
" Name: pB0015_DF_D_F\n",
336-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0015_DF/1\n",
335+
" Name: pJ23116_GB_B_G\n",
336+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23116_GB/1\n",
337337
" Strain: None\n",
338-
" Fusion Sites: ['D', 'F'] Antibiotic Resistance: Ampicillin\n",
338+
" Fusion Sites: ['B', 'G'] Antibiotic Resistance: Ampicillin\n",
339339
", Plasmid:\n",
340-
" Name: pJ23116_AB_A_B\n",
341-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23116_AB/1\n",
340+
" Name: pJ23100_FB_B_F\n",
341+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pJ23100_FB/1\n",
342342
" Strain: None\n",
343-
" Fusion Sites: ['A', 'B'] Antibiotic Resistance: Ampicillin\n",
343+
" Fusion Sites: ['B', 'F'] Antibiotic Resistance: Ampicillin\n",
344344
"]\n",
345345
"Backbones: [Plasmid:\n",
346-
" Name: DVK_FG_F_G\n",
347-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/DVK_FG/1\n",
348-
" Strain: None\n",
349-
" Fusion Sites: ['F', 'G'] Antibiotic Resistance: Kanamycin\n",
350-
", Plasmid:\n",
351-
" Name: DVK_AE_A_E\n",
352-
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/DVK_AE/1\n",
353-
" Strain: None\n",
354-
" Fusion Sites: ['A', 'E'] Antibiotic Resistance: Kanamycin\n",
355-
", Plasmid:\n",
356346
" Name: DVK_GH_G_H\n",
357347
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/DVK_GH/1\n",
358348
" Strain: None\n",
@@ -362,6 +352,16 @@
362352
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/DVK_EF/1\n",
363353
" Strain: None\n",
364354
" Fusion Sites: ['E', 'F'] Antibiotic Resistance: Kanamycin\n",
355+
", Plasmid:\n",
356+
" Name: DVK_FG_F_G\n",
357+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/DVK_FG/1\n",
358+
" Strain: None\n",
359+
" Fusion Sites: ['F', 'G'] Antibiotic Resistance: Kanamycin\n",
360+
", Plasmid:\n",
361+
" Name: DVK_AE_A_E\n",
362+
" Definition: https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/DVK_AE/1\n",
363+
" Strain: None\n",
364+
" Fusion Sites: ['A', 'E'] Antibiotic Resistance: Kanamycin\n",
365365
"]\n"
366366
]
367367
}
@@ -382,7 +382,7 @@
382382
},
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{
384384
"cell_type": "code",
385-
"execution_count": 6,
385+
"execution_count": 33,
386386
"id": "9cdd18d0",
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"metadata": {},
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"outputs": [],
@@ -404,7 +404,7 @@
404404
},
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{
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"cell_type": "code",
407-
"execution_count": 7,
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"execution_count": 34,
408408
"id": "d76dbdeb",
409409
"metadata": {},
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"outputs": [
@@ -459,7 +459,7 @@
459459
},
460460
{
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"cell_type": "code",
462-
"execution_count": 8,
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"execution_count": 35,
463463
"id": "3bcf02fb",
464464
"metadata": {},
465465
"outputs": [
@@ -469,7 +469,7 @@
469469
"'Valid.'"
470470
]
471471
},
472-
"execution_count": 8,
472+
"execution_count": 35,
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"metadata": {},
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"output_type": "execute_result"
475475
}
@@ -480,7 +480,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"execution_count": 36,
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"id": "47bcde97",
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"metadata": {},
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"outputs": [
@@ -768,16 +768,16 @@
768768
},
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{
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"cell_type": "code",
771-
"execution_count": 17,
771+
"execution_count": 37,
772772
"id": "66b401f9",
773773
"metadata": {},
774774
"outputs": [
775775
{
776776
"name": "stdout",
777777
"output_type": "stream",
778778
"text": [
779-
"https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pE0040_CD/Fusion_Site_C_2/1\n",
780-
"https://synbiohub.org/user/Gon/CIDARMoCloParts/Fusion_Site_C_sequence/1\n"
779+
"https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pE0040_CD/dva_backbone_core_5/1\n",
780+
"https://synbiohub.org/user/Gon/CIDARMoCloParts/dva_backbone_core_seq/1\n"
781781
]
782782
}
783783
],
@@ -793,9 +793,93 @@
793793
},
794794
{
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"cell_type": "code",
796-
"execution_count": null,
796+
"execution_count": 38,
797797
"id": "32dddc4d",
798798
"metadata": {},
799+
"outputs": [
800+
{
801+
"name": "stdout",
802+
"output_type": "stream",
803+
"text": [
804+
"l0: ['Fusion_Site_B_2', 'B0034_3', 'Fusion_Site_C_4', 'dva_backbone_core_5']\n",
805+
"l1: ['Ligation_Scar_C', 'dvk_backbone_core', 'Ligation_Scar_D', 'Ligation_Scar_A', 'B0015', 'B0034', 'Ligation_Scar_B', 'E0030_yfp', 'J23100', 'Ligation_Scar_E']\n"
806+
]
807+
}
808+
],
809+
"source": [
810+
"l0_plas = plas_doc.get(\n",
811+
" \"https://synbiohub.org/user/Gon/CIDARMoCloPlasmidsKit/pB0034_BC/1\"\n",
812+
")\n",
813+
"l1_plas = transformation_doc.get(\n",
814+
" \"https://synbiohub.org/user/Gon/buildplanner_bacteerial_transformation/composite_1/1\"\n",
815+
")\n",
816+
"\n",
817+
"print(\"l0:\", [comp.displayId for comp in l0_plas.getInSequentialOrder()])\n",
818+
"print(\"l1:\", [comp.displayId for comp in l1_plas.components])"
819+
]
820+
},
821+
{
822+
"cell_type": "code",
823+
"execution_count": 39,
824+
"id": "e4cddafc",
825+
"metadata": {},
826+
"outputs": [],
827+
"source": [
828+
"from buildcompiler.constants import PART_ROLES\n",
829+
"\n",
830+
"\n",
831+
"def is_single_part(plasmid: sbol2.ComponentDefinition, sbh) -> bool:\n",
832+
" num_components = len(plasmid.components)\n",
833+
"\n",
834+
" if num_components != 4:\n",
835+
" return False\n",
836+
" else:\n",
837+
" component_definitions = [\n",
838+
" get_or_pull(sbol2.Document(), sbh, comp.definition)\n",
839+
" for comp in plasmid.getInSequentialOrder()\n",
840+
" ]\n",
841+
"\n",
842+
" for index, comp in enumerate(component_definitions):\n",
843+
" if bool(set(comp.roles) & set(PART_ROLES)): # identify part index\n",
844+
" previous_component = component_definitions[(index - 1) % num_components]\n",
845+
" next_component = component_definitions[(index + 1) % num_components]\n",
846+
" print(previous_component, comp, next_component)\n",
847+
"\n",
848+
" if (\n",
849+
" RESTRICTION_ENZYME_ASSEMBLY_SCAR in previous_component.roles\n",
850+
" and RESTRICTION_ENZYME_ASSEMBLY_SCAR in next_component.roles\n",
851+
" ):\n",
852+
" return True\n",
853+
"\n",
854+
" return False"
855+
]
856+
},
857+
{
858+
"cell_type": "code",
859+
"execution_count": 40,
860+
"id": "8def50e5",
861+
"metadata": {},
862+
"outputs": [
863+
{
864+
"name": "stdout",
865+
"output_type": "stream",
866+
"text": [
867+
"https://synbiohub.org/user/Gon/CIDARMoCloParts/Fusion_Site_B/1 https://synbiohub.org/user/Gon/CIDARMoCloParts/B0034/1 https://synbiohub.org/user/Gon/CIDARMoCloParts/Fusion_Site_C/1\n",
868+
"True\n",
869+
"False\n"
870+
]
871+
}
872+
],
873+
"source": [
874+
"print(is_single_part(l0_plas, buildcompiler.sbh))\n",
875+
"print(is_single_part(l1_plas, buildcompiler.sbh))"
876+
]
877+
},
878+
{
879+
"cell_type": "code",
880+
"execution_count": null,
881+
"id": "00d7a782",
882+
"metadata": {},
799883
"outputs": [],
800884
"source": []
801885
}

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