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update demo notebook
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@chungmuen
chungmuen committed Nov 28, 2024
1 parent 1582f83 commit 5116a21
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23 changes: 23 additions & 0 deletions demo/demo_in.txt
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GENE_NAME=TPP123
SEQUENCE=MVSVIKEEMKIKLRMEGTVNGHNFVIEGEGKGNPYEGTQTMDLKVTEGGPLPFAYDILSPQFMYGSKAFIKYPADIPDYFKQSFPEGFHWERVMTYEDGGVCTATQNTSLRGDCFFYDVRFDGVNFPPNGPVMQKKTLGWEPSTEKMYVRDGVLKGDVIKALLLEGGGHYRCDFKTTYKAKKDVRLPGYHFVDHRIEILKHDKDYNKVKQYENAVARYSMLPSQAK
FIX_DNA_SEQUENCE=ATGGTTAGCGTGATCAAAGAAGAGATGAAAATCAAACTGCGTATGGAAGGCACCGTGAATGGTCATAATTTTGTGATTGAAGGTGAAGGCAAAGGCAATCCGTATGAAGGTACACAGACCATGGATCTGAAAGTTACCGAAGGTGGTCCGCTGCCGTTTGCATATGATATTCTGAGTCCGCAGTTTATGTATGGCAGCAAAGCCTTTATCAAATATCCGGCAGATATCCCGGATTACTTTAAACAGAGCTTTCCGGAAGGTTTTCATTGGGAACGTGTTATGACCTATGAAGATGGTGGTGTTTGTACCGCAACACAGAATACCAGCCTGCGTGGTGATTGTTTCTTTTATGATGTTCGTTTTGATGGCGTGAACTTTCCGCCTAATGGTCCGGTTATGCAGAAAAAGACCTTAGGTTGGGAACCGAGCACCGAGAAAATGTATGTTCGTGATGGTGTTCTGAAAGGCGACGTTATTAAAGCACTGCTGCTGGAAGGTGGTGGTCATTATCGTTGTGATTTCAAAACCACCTACAAAGCCAAAAAGGATGTTCGTCTGCCTGGTTATCATTTTGTGGATCATCGTATCGAAATCCTGAAACACGATAAGGACTACAACAAAGTGAAACAGTATGAAAATGCCGTTGCGCGTTATAGCATGCTGCCGAGCCAGGCCAAA
CUT_NUMBER_RANGE=(3,4)
MIN_AA_LENGTH=6
MAX_COST=50000
MAX_LENGTH_UNEVENNESS=5
MIN_LIGATION_FIDELITY=0.99
SATISFACTION_LIGATION_FIDELITY=0.99
FIDELITY_DATA=FileS01_T4_01h_25C.xlsx
HOST=p_pastoris
FUSION_SITES_USED_BY_BACKBONE=('CTTG', 'TAGC', 'CCAT', 'CGCT', 'TAAT')
DNA_5_PRIME=AATTTGAAGACAA
DNA_3_PRIME=TAATAAATTTGTCTTCTTTAA
ALLOWED_CUT_POSITIONS=(70,75),(105,110),(145,150),(160,162),(180,185)
COST_PER_BP=0.1
MIN_DNA_LENGTH=100
MAX_DNA_LENGTH=10000
MODULE_PLATE_FORMAT=96
ENZYME=BpiI
BACKBONE_SIZE=3000
MUTATIONS=[{'position': 63, 'aa': ['L', 'H']}, {'position': 80, 'aa': ['W', 'L']}, {'position': 143, 'aa': ['F', 'I']}, {'position': 158, 'aa': ['A', 'I', 'N']}, {'position': 174, 'aa': ['A', 'I']}, {'position': 194, 'aa': ['F', 'Y']}]
LINKED_MUTATIONS=[(('M', 63, 'H'), ('F', 80, 'L')), (('M', 63, 'L'), ('F', 80, 'W'))]
40 changes: 20 additions & 20 deletions demo/seqTeleporter_demo.ipynb
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Expand Up @@ -72,9 +72,9 @@
"SCRIPT_DIR = os.path.dirname(os.path.abspath('__file__'))\n",
"sys.path.append(os.path.dirname(SCRIPT_DIR))\n",
"\n",
"from proseqteleporter.utils.utils import print_available_resources\n",
"from proseqteleporter.main_libs import (generate_and_optimize_ready_to_click_modules,\n",
" assemble_modules_and_generate_robot_instruction)\n",
"from seqteleporter.utils.utils import print_available_resources\n",
"from seqteleporter.main_libs import (generate_and_optimize_ready_to_click_modules,\n",
" assemble_modules_and_generate_robot_instruction)\n",
"\n",
"print(f'Here is: {SCRIPT_DIR}')"
]
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"\u001B[1mFIX_DNA_SEQUENCE=\u001B[0mATGGTTAGCGTGATCAAAGAAGAGATGAAAATCAAACTGCGTATGGAAGGCACCGTGAATGGTCATAATTTTGTGATTGAAGGTGAAGGCAAAGGCAATCCGTATGAAGGTACACAGACCATGGATCTGAAAGTTACCGAAGGTGGTCCGCTGCCGTTTGCATATGATATTCTGAGTCCGCAGTTTATGTATGGCAGCAAAGCCTTTATCAAATATCCGGCAGATATCCCGGATTACTTTAAACAGAGCTTTCCGGAAGGTTTTCATTGGGAACGTGTTATGACCTATGAAGATGGTGGTGTTTGTACCGCAACACAGAATACCAGCCTGCGTGGTGATTGTTTCTTTTATGATGTTCGTTTTGATGGCGTGAACTTTCCGCCTAATGGTCCGGTTATGCAGAAAAAGACCTTAGGTTGGGAACCGAGCACCGAGAAAATGTATGTTCGTGATGGTGTTCTGAAAGGCGACGTTATTAAAGCACTGCTGCTGGAAGGTGGTGGTCATTATCGTTGTGATTTCAAAACCACCTACAAAGCCAAAAAGGATGTTCGTCTGCCTGGTTATCATTTTGTGGATCATCGTATCGAAATCCTGAAACACGATAAGGACTACAACAAAGTGAAACAGTATGAAAATGCCGTTGCGCGTTATAGCATGCTGCCGAGCCAGGCCAAA\n",
"\u001B[1mFUSION_SITES_USED_BY_BACKBONE=\u001B[0m('CTTG', 'TAGC', 'CCAT', 'CGCT', 'TAAT')\n",
"\u001B[1mHOST=\u001B[0mp_pastoris\n",
"\u001B[1mFIDELITY_DATA_PATH=\u001B[0mC:\\Users\\GOFKV\\PycharmProjects\\seqTeleporter\\proseqteleporter\\data\\neb_fidelity_data\\FileS01_T4_01h_25C.xlsx\n",
"\u001B[1mFIDELITY_DATA_PATH=\u001B[0mC:\\Users\\GOFKV\\PycharmProjects\\seqTeleporter\\seqteleporter\\data\\neb_fidelity_data\\FileS01_T4_01h_25C.xlsx\n",
"\u001B[1mMUTATIONS=\u001B[0m[{'position': 63, 'aa': ['L', 'H']}, {'position': 80, 'aa': ['W', 'L']}, {'position': 143, 'aa': ['F', 'I']}, {'position': 158, 'aa': ['A', 'I', 'N']}, {'position': 174, 'aa': ['A', 'I']}, {'position': 194, 'aa': ['F', 'Y']}]\n",
"\u001B[1mLINKED_MUTATIONS=\u001B[0m[(('M', 63, 'H'), ('F', 80, 'L')), (('M', 63, 'L'), ('F', 80, 'W'))]\n",
"\u001B[1mCUT_NUMBER_RANGE=\u001B[0m(3, 4)\n",
Expand All @@ -207,7 +207,7 @@
"--------------------------------------------------------------------------------------------------\n",
"\u001B[1m Results For 4 Fragments: \u001B[0m\n",
" Number of cuts: 3 \n",
" Elapsed time: 4.33 \n",
" Elapsed time: 2.38 \n",
" Number of partitions checked: 216\n",
" Number of unique partitions checked: 216\n",
" Number of unique partitions violating hard constraints: 0\n",
Expand Down Expand Up @@ -259,15 +259,15 @@
" <AG|GC>G[KKDVRLPGYHFVDHRIEILKHDKDYNKVKQYENAVARYSMLPSQAK]\n",
"--------------------------------------------------------------------------------------------------\n",
"\u001B[1m Result \"best_partitions_by_cut_number\" is exported at:\n",
" C:\\Users\\GOFKV\\PycharmProjects\\seqTeleporter\\demo\\input_2024-10-10output\\logs\\best_partitions_by_cut_number_dist_mut_1.json\u001B[0m\n",
" C:\\Users\\GOFKV\\PycharmProjects\\seqTeleporter\\demo\\input_2024-11-28output\\logs\\best_partitions_by_cut_number_dist_mut_1.json\u001B[0m\n",
"--------------------------------------------------------------------------------------------------\n",
"\u001B[1m Result \"params\" is exported at:\n",
" C:\\Users\\GOFKV\\PycharmProjects\\seqTeleporter\\demo\\input_2024-10-10output\\logs\\params_dist_mut_1.json\u001B[0m\n",
" C:\\Users\\GOFKV\\PycharmProjects\\seqTeleporter\\demo\\input_2024-11-28output\\logs\\params_dist_mut_1.json\u001B[0m\n",
"\n",
"\u001B[1m\n",
"===========================================================================================\n",
" SUCCESSFULLY IDENTIFIED OPTIMAL PARTITIONS! \n",
" Total elapsed time: 4.35 seconds\n",
" Total elapsed time: 2.39 seconds\n",
"===========================================================================================\u001B[0m\n",
"\u001B[1m===========================================================================================\u001B[0m\n",
" \u001B[1m GENERATING MODULES \u001B[0m \n",
Expand All @@ -291,30 +291,30 @@
" Validating dna fragment constraints (enzyme sites)...\n",
" Passed validation of mutant dna fragments constraints!\n",
"Validating mutant dna fragments by in-silico assembly...\n",
"Random combi in-silico assembly: M63L_F80W_S143I_V158A_F174I_H194Y, \n",
"Random combi in-silico assembly: M63H_F80L_S143I_V158N_F174I_H194F, \n",
" Validation Passed: True\n",
"Random combi in-silico assembly: F174I_H194F, \n",
"Random combi in-silico assembly: S143F_V158I_F174I, \n",
" Validation Passed: True\n",
"Random combi in-silico assembly: M63L_F80W_S143I_V158A_H194F, \n",
"Random combi in-silico assembly: M63L_F80W_V158I_H194Y, \n",
" Validation Passed: True\n",
"Random combi in-silico assembly: M63L_F80W_V158A_F174I_H194Y, \n",
"Random combi in-silico assembly: M63L_F80W_S143I_V158A_F174I_H194F, \n",
" Validation Passed: True\n",
"Random combi in-silico assembly: M63H_F80L_S143I_V158A_F174A, \n",
"Random combi in-silico assembly: M63L_F80W_V158N_F174I_H194Y, \n",
" Validation Passed: True\n",
"Random combi in-silico assembly: S143I_V158I_F174A_H194Y, \n",
"Random combi in-silico assembly: wild_type, \n",
" Validation Passed: True\n",
"Random combi in-silico assembly: M63H_F80L_S143I_V158I_F174A_H194F, \n",
"Random combi in-silico assembly: V158A_F174A_H194F, \n",
" Validation Passed: True\n",
"Random combi in-silico assembly: S143F_V158A_F174I_H194F, \n",
"Random combi in-silico assembly: M63L_F80W_S143F_F174A, \n",
" Validation Passed: True\n",
"Random combi in-silico assembly: M63L_F80W_S143F_V158A_F174I_H194Y, \n",
"Random combi in-silico assembly: M63H_F80L_S143I_V158A_H194F, \n",
" Validation Passed: True\n",
"Random combi in-silico assembly: M63L_F80W_S143I_F174I, \n",
"Random combi in-silico assembly: V158A_F174A_H194F, \n",
" Validation Passed: True\n",
"Exporting DNA module ordering sheet\n",
"--------------------------------------------------------------------------------------------------\n",
"\u001B[1m DNA module ordering sheet is exported at:\n",
" C:\\Users\\GOFKV\\PycharmProjects\\seqTeleporter\\demo\\input_2024-10-10output\\results\\order_modules_4fragments.xlsx\u001B[0m\n",
" C:\\Users\\GOFKV\\PycharmProjects\\seqTeleporter\\demo\\input_2024-11-28output\\results\\order_modules_4fragments.xlsx\u001B[0m\n",
"\n",
"\u001B[1m\n",
"================================================================================================\n",
Expand Down Expand Up @@ -370,7 +370,7 @@
"The README sheet is validated!\n",
"\n",
"Plate mapping sheet is exported to:\n",
" C:\\Users\\GOFKV\\PycharmProjects\\seqTeleporter\\demo\\input_2024-10-10output\\results\\2024-10-10_source_destination_plate_map.xlsx\n",
" C:\\Users\\GOFKV\\PycharmProjects\\seqTeleporter\\demo\\input_2024-11-28output\\results\\2024-11-28_source_destination_plate_map.xlsx\n",
"\n",
"Preview of mapping sheet: \n",
" Source Plate Target Plate Source Well Target Well Volume_ul \\\n",
Expand Down

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