JSON Schemas¶
JSON inputs and schemas for DASi.
Default Cost Parameters¶
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 | {"_primer_min_span": -300,
"_synthesis_left_span_range": [-500, 500],
"_synthesis_step_size": 10,
"global_material_modifier": 1.0,
"global_time_cost": 10.0,
"primer_cost": {"columns": ["name",
"min",
"max",
"base cost",
"cost per bp",
"time (days)"],
"data": [["IDTPrimer", 16.0, 60.0, 0.0, 0.15, 1.5],
["IDTUltramer", 45.0, 200.0, 0.0, 0.4, 1.5]]},
"primer_efficiency": {"columns": ["min", "max", "efficiency"],
"data": [[0, 10, 0.0],
[10, 15, 0.3],
[15, 20, 0.6],
[20, 30, 0.8],
[30, 40, 0.9],
[40, 45, 0.9],
[45, 50, 0.8],
[50, 100, 0.75],
[100, 120, 0.5],
[120, 150, 0.3],
[150, 250, 0.1],
[250, 300, 0.0]]},
"primer_min_anneal": 16,
"synthesis_cost": {"columns": ["min", "max", "base", "time"],
"data": [[0, 1, 0, 0],
[1, 100, "inf", "inf"],
[100, 500, 89.0, 3.0],
[500, 750, 129.0, 3.0],
[750, 1000, 149.0, 4.0],
[1000, 1250, 209.0, 7.0],
[1250, 1500, 249.0, 7.0],
[1500, 1750, 289.0, 7.0],
[1750, 2000, 329.0, 7.0],
[2000, 2250, 399.0, 7.0]]}}
|
Cost Parameter Schema¶
The JSON schema for the Cost Model input. Initialize the cost model using:
from dasi.cost import SpanCost
# open custom parameters
cost_model = SpanCost.open('my example.json')
# open default parameters
cost_model = SpanCost.open()
Cost Parameters Schema¶
This schema validate a json input for the DASi cost model |
|||||
type |
object |
||||
properties |
|||||
|
global time cost |
||||
the global cost of waiting 1 day |
|||||
type |
number |
||||
|
global material modifier |
||||
multiplies the effect of the material cost by this amount |
|||||
type |
number |
||||
examples |
1 |
||||
default |
1 |
||||
|
minimum primer anneal |
||||
the minimum number of bases to consider for an annealing event |
|||||
type |
number |
||||
multipleOf |
1.0 |
||||
maximum |
99 |
||||
minimum |
5 |
||||
default |
16 |
||||
|
type |
number |
|||
multipleOf |
1.0 |
||||
|
primer efficiency data frame |
||||
provides efficiency homology for gibson assembly |
|||||
type |
object |
||||
properties |
|||||
|
type |
array |
|||
items |
type |
array |
|||
items |
|||||
type |
number |
||||
multipleOf |
1 |
||||
type |
number |
||||
multipleOf |
1 |
||||
type |
number |
||||
maximum |
1 |
||||
additionalItems |
False |
||||
|
type |
array |
|||
items |
type |
string |
|||
maxItems |
3 |
||||
minItems |
3 |
||||
uniqueItems |
True |
||||
additionalProperties |
False |
||||
|
type |
object |
|||
properties |
|||||
|
type |
array |
|||
items |
type |
array |
|||
maxItems |
6 |
||||
minItems |
6 |
||||
|
type |
array |
|||
items |
type |
string |
|||
maxItems |
6 |
||||
minItems |
6 |
||||
uniqueItems |
True |
||||
additionalProperties |
False |
||||
|
type |
object |
|||
properties |
|||||
|
type |
array |
|||
items |
type |
array |
|||
maxItems |
4 |
||||
minItems |
4 |
||||
|
type |
array |
|||
items |
type |
string |
|||
maxItems |
4 |
||||
minItems |
4 |
||||
uniqueItems |
True |
||||
additionalProperties |
False |
||||
|
type |
number |
|||
multipleOf |
1.0 |
||||
|
type |
array |
|||
items |
|||||
type |
number |
||||
multipleOf |
1.0 |
||||
type |
number |
||||
multipleOf |
1.0 |
||||
additionalItems |
False |
||||
additionalProperties |
False |
||||
maxProperties |
9 |
||||
minProperties |
9 |
Design Output Schema¶
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 | {
"metadata": {
"program": "dasi",
"version": "0.2.1",
"execution_trace": {
"compile": {
"__name__": "compile",
"__spec__": "FullArgSpec(args=['self', 'post_process_kwargs'], varargs=None, varkw=None, defaults=(None,), kwonlyargs=[], kwonlydefaults=None, annotations={'post_process_kwargs': typing.Dict})",
"start": "2021-02-23 12:12:46.881306",
"end": "2021-02-23 12:12:47.075038",
"args": {
"post_process_kwargs": null
},
"algorithm": "standard optimization"
},
"optimize": {
"__name__": "optimize",
"__spec__": "FullArgSpec(args=['self', 'n_paths'], varargs=None, varkw=None, defaults=(3,), kwonlyargs=[], kwonlydefaults=None, annotations={'return': typing.Dict[str, dasi.design.design_result.DesignResult]})",
"start": "2021-02-23 12:12:47.075159",
"end": "2021-02-23 12:12:47.091454",
"args": {
"n_paths": 1
},
"algorithm": "standard optimization"
}
}
},
"designs": {
"0b9d1c89-0289-4bbc-b650-613e678918d7": {
"compiled": true,
"run": true,
"success": false,
"assemblies": [],
"record": {
"name": "<unknown name>",
"length": 9438,
"id": "<unknown id>",
"is_circular": true
},
"sequence": {
"bases": "TACTTTGTAGAATACATCACTGAACGAGGTAGTCTCGTTGAATCGCTGCGATGGTCGACAGATTACGCTCGATAGCGGTGGGCAAGCGGAAAGGAGTCATACCACGTCAATTAAAGATGCTACCTGCGAACTGTGGTACCATGATAGATCAGTTCCGTCTTCATTGGTTAGTCGACGTGGAAAACGCTTCTAAGGACGCTACGAGAATAGATCCAACTCGGTGGCAAGACCTCGCGGATACTCCACAAATCTACTGACACGGCCTGCTTGTGTACCGCTGATGAACGTCGTGTTGCTAACTGACTACCGGTACCTGTAGACTGTTTGTGCGACCTAGCCTGTGAAAGGCCTTAGGCGAGACTACAGTACTACCCGCCTTGGAGGAGAGCCGGGGCAGGTGTTCCCACGCCCATACGAAAAGATACACAATTCCAAGTGACGTGCTTGAGAAGAGAACACAGCATGCTACAGGGATTACACGCTAAATCATCCTTACATTCTGGAGCTTTGAGTCAATCTCTGAACTGCCGGCCGCTCCATCCTGTAGTGCAACCGTCCAGAATGAATGGGTTCTCTCAAGGGAATCCAGCTATTCCAGTTTCCTTTCCTGCGTGATCATAATAGCAGTTGACCTATATGCCTTCTACGTGCCATGTCACCCCGAGGAATTTTGAAGTAGATCTACGGGCAACAGAGACCAGGAGATGGATTGAATACGAATTGAAAACAATTAATAGGTTGCTCTGAAATTCACAAGAAGGAGGTGAATGCCTCATCACGCGCCTATAATCCTAGTACAGTTCCGTCCACAGGTAAGCTTTATTTACGACTCGAGGGTCACTGACCACAAAACCACAAGCTACTGAGGTTCTGCCAGGAAGGTGGTGGCCGCCTCTGCAATCGTCCAGCGTCTCCGTCCTCATTCATGTAACATACTCTGGTGGCGCTTCCAAATGATACAATCCAGGTTGGATGGTGTTAGTTATCAACACCAGGGCAATCTGCCCTATAACGACTTTCTCATGAACCTGCAATGCTTCCTCACTCCATGGGCAACCTTGCTTAAATCATACAGACGAGCGTTATCTATTCATACAGAAATGTCCAAGGGGGGACGCCGCAGAACGATGTATGTAAGGGTTTAATACCGGCAATTATGCTAAGTCGGCCAGGCGACGGAGTGGATTACGTCACTCGTCTCCGATAAGCTCTGGGTAGAGCCAATGACCATTGTTGTGAGAGTCATCTTGCCCTGGAGCAGCAACCCGCAGACATTCATAGTTAACAGCCGCCTGGATTGGATCCGTCAGGTAGAATGGAAGCCGTCAACAAGCTAGGCCCATCATCCCATATCAGGATCCAAGGATATGCGATCCGGGTCCAGACCTGTGCTACCACATCCTATTCTATGCAGCTTTCGTTTAAGAAACAAGCCTAAGACGGTTGCATGAATAGTTGTGGTAAGCTATCCTAGGGTTAGTCTCAGCCCGATGAGGATATCGGGCCTAGTTCATGGATGTGTACACGCGTCACCTTGAGCGGATCTGGTATATGGGAAAGACCTTCCAAGAGGTGAATCACTCCCTGTATTGGCTTCAGGCCCATGTAAAACTCGCGGTAACCACATATGGACAGCAGTTCGAAGTTGTCTGAATTACCATGTAAGAGACTGGGACACACCAAAGGAAGGGAGCCTCCCCCCAATTGCACGCTGTTATGGTAATACCTTCTAGTAGCCTGTTGTGTAGGGCTTTGAAGGCTTGTCTTCTACTGACGAGGGTTGAAGGAAATTGTGAGATTTCATCGACCGGCGCCCCATTTGATTGCAATTGGAAACCCCGACAGCCACAATTGACCATAGTCACTACCTGCCCCGCGAGAGCTTATCGGTGATATTCGTTTACTAAGGTTTTACGGAGTGTCACCAAGTTTCACTTCCAACTTCCTATCCATATTCTTAACGATGCTACAAATACCTAGCCAACGCCCTTAAGGGGTTATTGACGCGTCGTAATAACGTCTTGTAGAGGGCACCATTGGAGCTTGTGTAGAGTGGGCCACTGAAACCTCGAGCTACCCAGAAAATACGATCCTGGACGTACCAAACTTCGCTCGTATACTCCTGGAATATCTTGGCATTTTCCCGCATAATACAGTATCTAGGATTCGTACGTAGGGCCACCAGCTTACTGCCTTTGGTCGCCACACAAGACCCAAGCCGAAACGGCGTTTCCAATATTCGTACTACCACTGGCGCCATTGGACATCGTATGGGTGTCTTTCGCTCGCACCATAACGCACGCAGTTTACTAGATCTCATCGCCTCCACGAGTAGCTTGGGTGTTTGGACATTGGCGTGGCGTGTACTGGGATGGCAAAAAAACTAGTTTGTGTTGTCGACCGAGGCAGTACTAAATGCCTGTCATAGAGGTTTGAACATCATTACAGGAAACCTCCCCTTGTGGAACGAACGCCTGCCATTCGGTGATGAGTAGAGGATGTGAGGCGTGTTCTCTAGTATGCTTAGGATGTATATTCCTCCCCACGCCTCCTCGTCTGGCAATTGCAGTTACTCCTACTACCGGGTCTCCGTTGAATTCGGAAGACCTGGTGGACTCGCGCGATTTTGAAAATGAAACCTTGAGGAGTTTTTAAACATAGCCCTTCGCCCCACTTAAACGGTACAATACCCTGGGGGCAACTTCGACAACGTTGTACATCACGGAGACTGAAGAACACTATTGGGTACCCATATATACGAGAGCCACATTATGGGCGGTTCGAAGCCAATTATCTTAGAATAGTCTGACTAGGTCCGGCACTTTCCCAGAAAGCACCAATTTTGGTGAGCTGCACAATTCCACACGTGGTAATAGCATATGGGGGCTCTTTGATACGAAAGAACTATGTGAAACCTAACTATTGTTGCTGACTGATGTCCTAACGAGGACTAGGATTTAGGCCTCATACGCAGTTTGTTCTGGAAGCGTGGAAAATATCGTACAACACATAAGCTCACCTAAATCTACTACAGTGACTTGTCCACGAAAATATGGAGGTGAGTGTCATCGTTAACTTAAAAGGGCACAACGGTCGGCGTGAGCTGCGGACTGATTTGGCGACAACTGGGCGCATGCTCTTCTAAAAACGGTGGACACCGCCTCTATAGAGCACTCCTAATGCTTGAAACTCGGCGGCCTGTGAGCAGCAACGGGATTTGGTCATTACAACTTACCCAAGGCCCCATCCGTCTAAGTGTTAAAGCTTTTAGGAAGCTATCTATTCTAGATTTACAGCGATCCAGCTACAGGACTATCTTCGCTTGGAACATACTACTGGGGAACTTGCTGCCAAAAAAATAGGCTCCTCTTATTAAGCCAATTTGCAATTGGAGACATGGGCACTGTCAGTTTTGCAGTTACGTAGTCAGCGGCCTTTACACTACAACCACGTGGGTTCATTTTCAGGGCCACCACCCAGCCTTGAACAGCGCAGAGGGGAGTTCTGATTAACTCTTTCAAGCTTCCTTTATGGGAGCCTTTAAAGGATTCTTTTTCCCTGGGCCATTAATTCAAACGCCATGTGCTCAACCTTGCTACTAACAGCTTCCTTGACCGTGTGGAGTTGCCAATGGGCTTCGCACTATGTTGCTAACAGCAGCCGTAACCGACGTGTACTCAATTTGTTTCCTGATAGCAACGTTAGCTCGTCCATTAGGATTTTAAGCCTCCATCCTCACCAGGGAGGGTCCGTCGCGAGGGCGCAATTGTCTATGGGATTGGACTGTCTTCCTGCATACCTGAGTCGTCAGGAGCCTGATTATATAGGTGGAGATACGGAGAGTGAGCCAAATTCTCACATTGGGGGACGCGTTGAGTAATGCTGGGCTCGTATCTCGTAGACAGACACGCTCCTTTATCCGTTGTATCGTTCTGGAGTGAGCGAAGCGATTGATCCACCTCCTGCCCATTACCGAGTTATGACACCTACAGTGGTTTCTCAGTGATGCCATTGGACTAAGTGGTTGCTCCTTTTCTCCTGAATGTCCGCTGGAGGCCTATCCTGGCGGATCAGTTGAAGGTCAATCGTTTACTTCGCGTTGTGCCAGGAGTCCGTGACCGTCGGAAATTTGTTCATACATGTGCTGCGCTCGCGTTAAAAAGACGGCGTGTTTCCAGAGTGGCTACACCGCTTCGAACTAGGCTAGATTACCGCGGTGCTCGGGCAAAAAGCTTCATTTTTTCCCCGAGACTCATCCCGGATCGCGAAAACCATGCGAGAATCACAAAGTGGAAGTAAATTGCTGGTTTCGTCGAACGCCATATCGACCCCGCTTTGGACAAAGCCACATGCCTAGACACGGCGACATACCGAATTATAGGACGAAGTACAATTCTGACCCGTTTGAGTCCTCAAAGAAAGTGCCCTATTGACAAAAAAGCAATTGCGACATAGGCCGCTATTGTCGGTGGAACAGTCTAAGTGCTCCAGCCTTTACTACTTGGCAGCGGGGCTACTGCCCTGCCCACAATTATCAGAAGGCTTGTACCCTAGATGAGGAAGGGTATAAGGGTATCAGCCATACGCGTACTCCGATGGTCTCTAAAGTTTTTATACCCCCGTTAATATATTCAAAGACACACCCAAAGAGGGAATACCGCATTCGGGGAGCTCCGCCCGCATATATGAGAGTTCGGCCGAACCTAATAGGTCATAGTCGAAACTGGTGACTATAAGTTGGTACATGACGGGCAATTATCTACGAATAGCTAAGCAGCGGTCAATAAACGGCCGACGCCCCCAGCCCATCGTTTTGAAAGAGGGGGAATATTGAGCTGGATCCGGTGTCACTTATTCCACCAACCATTATGGTAAATTATAGGCTGCATGCATACAAAGTACCTATGGCCCTTTAGAAAACTTGGGATCTCTCACTCCTTGCTCGTACTTTCGCACGGTAGGGCCACAGGATCGTAAATAGTGCTTTGAGGCTCTGTCCATCCTTGATGGCCCTGCGTGGGCCAGATCAGGATGAGGAGTTTGACAAATTGTGTGGCCAATCGTTAAGCACTATTAGTCGCTGGTGCGAGAGGTGCTGCTCGTTTACGCAGGAGTTTCAGCCGTGTATCGGACCTGCAGGCGGCGACTGGTGAATCTTCCCACGGGAGATGCTGAGATGGATGTCTTAACACCAGAGATGACTCCTCCGATGTAACCTATTATTGAGTCTAATTGCTCAATTGTAGCGTTATTCAATAAGACGAATTATTACATCCGCTTAATCTGTTAGACCCCCGGGCAGCTACAGCTGTTCCGACATAGTCTTAACTCAGTATACGACTGTTGGCGGATGGATCATAGGAGTTCATTAGAGATACCAGTACGACTGTACTGGGAAAGGCTTGTCCTGTCAGTCATATCGAGGCGTGTCGACAATCGGTACGTGAACATGATCCACCGAACGGATGCGTCATCGAGAACGATCTGAATGCAATCACCTTACTCTAGGATGGTGATTCAAGACATGTTTTCTTCAGACCGACCCCACGGCGTACATTCGACTCCTGGATTTTGACGATGGTAAGAGCTCTTCTGTAGAACCTATCACTTGACCGTGAGACCAGGTGAGATGCAAGTTTAGTCACCGACTCTGCTGTGAGGAGTTGTAAGCGCCGGCTTCGACGTCGTGCATTGGTGAGACATGTTGCGTAAAACGCTTGTAATAATGCTCTATAAACCTAAGAACTTATCCCGGGTCACCCACTTCAATTCGATGGGCTGCACCTACGCATTTCGAAAAGAGCCGAATAGGCAGGAGGATGGAATGACGGAATTAGACGCTTTCCTATATATTTTTATCCTCTTGGCCATTATTGCCTCTGTGGCGTGCTTAATCGCCAACCCCCGTAGTATAGACTTTTTCCCACGCCATGAGACTCGCAGTTGAACACGGTGTGCGGCAAATTTCCGCGAAGTTTTGGGGCGAACCCGAATAGAACCAAGACAGTGAGCTGTACGATTTATGACGCAGCTTGGTTCGAAGCCTCCAGTCCTCTATAGGGTTCGCAGGGATACCGACTACGGCTGAGGTTATAGAAGCAGCTAGCAACTCTGAACCGCCCACATTTTTAGAAACACCGTCTGCAAGTCTCGATGGATAATAGAGGTGTGATTACATACTTAGGTATCCGACAATACACCTGTAGATTAGTAGTTATCCCGCAGTAAATGTCGCCCGGACGCATGTGAACACGCCAGACCGAGGAGTTCCTACTCGGCAGTTCGGGGTACTTATCACTAATCGCGCAGGACCAGGCCGGGCTGCCGTCTTCCATTAGTGACTATTCCGCAAAAAACTGAACTCTTCTAAGACCTGTGCTTGTTATTCCGCTCTTGCCCCCTGGTATTAAACCTTGTGTGAGCTGTTGCCCGGACGAGGAGCAGACTTTGTTTACTGTTTGCAGTAGGAGAGCGCTCTCTGAGAGACAACCGCGGAGCTACGTCCGGGTGTCGCCGTCCGGCCGATCGAAGCTGTGTCTGTCGGGACCTGTCATTTAAATCTCTGACAGCTACCACGTATGCAGAGACAAGTTCAGCCGTATGCGGGACAAACAGCCAGGAAAATCCTGCCGCTGACAACACGGGTCTGCATCATCAGGAACTCCGTGTATTTTTTCTGATGGTCTACTAAACTACGCAGGTTATTGGACAACGCGTCGGCACCTCGGTGGTACTCGGCTGGGGCGGAAGGACTTGACCGATATGTCACGCTTGAGGGGCTCAGGTTGCGCCCACAGTGTTTAAAGCTGGTTATATAAGGTGTTCGTGCTTCCTGCAGGTGTGAATCTGCACGAAGATCGTTGGACCCTCCTAAAACGGAATCTACTCACGGTCCAAAAGCCGAAACATCCAATCCAGTAGACGTGCCCCCACGAACTTCACCGGTAATACCGACATCGCCGGTCTTCGGAAGAAGCACAGCTTCACATGTGTGGACCCAAATTCTGGAACTCGACGGTCTCTGTGGCGTGTCATGACCTATCGCGCAATACATCCTTCTCAAAATCTAGAGCCGTAAGTAGAACAGAACTGTGGATACTTTAGTGCCAATAATAGTATCCTATGAACTTGACAGGTTCAACAAAAGCAGTTAAAGCCTGTGCCGATTCGGGAGAGCACCGAAAGAATGAGAGTGGAACCAAGCCTTGTCCTGGGCCTTTGCCGTAAGTGCCGGCCAGAGAACGCCCGTAACCCAAACGACTACCACAAATGTCGAGGTGCAGGGCGTCTATGATAGGTGACATAACAGTGAGATCATACAGACAAAGCGGAACCGCCAACGCTCCATTACTACTTTCAGTGCTACCTGCATTCGCACTGTCGACTCCGTTGGTAGGGGAAGCGGAATCGTGGGAACTACCCCAGTACTTTACAAGGCACAAGCTCTTCTGAGTACACCACTGTACGTGATGGTTCGCTGTGCACATCTCGAGCCAAGCGAACATTCACTCGGTGACACCCTAAGGCGTTTTAGCATTGCCGTTGCCACGTTCCTCTAATTTCTGCCGTTCCCGTGCAGATCCAACTCCCACCGTAGGGGGCGTTCAGATCTGCGCCGTAGTCAAATATAGCTTATCTTTGGTGGACCAAACCCTGCCCCTTGCTTATGAGGATCCTCGATGTTTAATGAACGTAGGCGGTCACGGGGGGGGGAGGAGACATGCGGCCCGAGTTAAATCGCCACCCACAGGGGCGATCTCTTCTGAGCTAGGTATTGTCATGGCTGGAGTGTAACACATATAAGACTGTAAGGAAGTATCGGAGCACAACCTATACTGAGTGGTCAAATAGAGGCATTCGTTCGCATTGCTGTACAGGCAGTCGATGTACCCGGGCTTCAGTTCTGTACGATCTTGGGATACAAAACGGTAGTCTTCCCGCGCTTATTAGAGGCCCATTACCTACCTCTCTAACACGGCTATGCACTCATGCGTACGCACGAGAGTAGATTCTTGAGTCGTGGCAGTACATCAAGGTGGCGGGCGAGTTTCATCCCTCGCTCCCAACTTTTCGGGGACAACATTTCGCCAAAAAAGTATCCGCCCAAATCTCGACAGACGTTCAAAAGTCAGATCCTTCAATGTGGTTTTTCCGAGCTATGGCTAGATAAGCCCCTAAAAGTCGCAGTTCCACTTCGCAGGTAACCGAACGTGTGTATTAATCCGGAATCATTGATTTGTTTCCTAATGGAGGTAATGCTGCAACATCAGTCAAACTCCCTGATGCCTCGGGCCAGTAGAGCCGCGCGGGATACCGTAGCAAGTCTACACGTCCCGCTCACGAGGGGTCCAGATGGCTATGACATGTCCTTCTTCAAATTGGTCATCACACGCCGTTGCGAAGTAACCGCTGAGTCCTCCGTTCCTTGAAAGGTCCCTCTCGGGTCACTTACGGACAACCACTGGACATAACGTATTCAGCCTCATGTGCACCGCTTGGCATCTTTCGGCTTTCATAACCTTATCCCTTCTGCTCGTGTGGCTCTTCTGATTTCCTACTTAAAAGGAATCATTCAGATCGAACACACGTACGTCTGGGAAGGGGATTCTAAGGAGGACTGTCAGTACAACTGTACCATTCAACGAGCGAGAGATTCTCATGACTTATTGTGCTCGTAGCACCTTGTCGTAACACTTCCATGCTACGCAAAACTGTCCTAGTCAGCTACACCAGAATCGATAGTGATTAACTAACAAGGGAAGGTAAGCCGTGGGCGTCGAGACTTTAACTGCTAAAGCGCGGTAAGTCACAACCTGGTATGGTGATCAACCCCACTTCAAAGCTCCTCTATCAAAAGGATGTGACTACTGGGTATAGCCTCAGGCTGCCTCTACTTTCGTCTTGCGGGGTGCGATTAGCAACACTTGGTAAGACTTCGATCATGAGCCTTGGCTACGACGCTACCAACACGCGTGTCGGTCCCTTTACCTCGGCAAGGGGACCTCAGGTGGCTAATTTTGAAATGACAATTAACTAGCCGTCGTACAGCAAAGCCTGTACGTGTACAGTCGGGAAAAGCTCTACGGGCCGCATCCGTAGTTTACCGGTCGATGGAGCCTTAGCACATACGCTGGGAGACGGATCAATAGAGGGTAAACGCACATTTAGGACGCCAGAACCTAATGAAATCCGATTAACAAAGTCCCGCACTACATAGACCGAAATGTCCGAATTTTCTCTTCCGGCGAAATGCGGCCCTATTGCTGGTAGATACTGTTTGTGCGTAGCGATTAATCATAGTTGAGAGTAACGCATCTAAGCGGCGGTTTTGCGATCTCGGTACACGTCGTTCGCGATCGTAGGCACGCAAATCTTCGGACCATCCAATTCACTCCGAGACAGGGCGTTGGGTCCTGGTCCGCATACGCTCTGTTCACA",
"length": 9438,
"name": "<unknown name>",
"id": "<unknown id>",
"annotations": [
{
"start": 78,
"end": 403,
"strand": -1,
"color": "#71da69",
"name": "433c",
"type": "misc_feature"
},
{
"start": 403,
"end": 1359,
"strand": -1,
"color": "#1a0920",
"name": "c321",
"type": "misc_feature"
},
{
"start": 1806,
"end": 1919,
"strand": -1,
"color": "#d7ab91",
"name": "12b6db9a-8990-41e1-937d-9fe561943606",
"type": "misc_feature"
},
{
"start": 1919,
"end": 2080,
"strand": -1,
"color": "#52582a",
"name": "27dcc7eb-7a84-4373-bd91-6451327416e9",
"type": "misc_feature"
},
{
"start": 2102,
"end": 2842,
"strand": -1,
"color": "#59f0d6",
"name": "3e4e",
"type": "misc_feature"
},
{
"start": 3463,
"end": 4352,
"strand": -1,
"color": "#432175",
"name": "ffef",
"type": "misc_feature"
},
{
"start": 4352,
"end": 4772,
"strand": -1,
"color": "#d566ac",
"name": "c422",
"type": "misc_feature"
},
{
"start": 6194,
"end": 6667,
"strand": -1,
"color": "#53788b",
"name": "a2c28aec-9fbb-474a-99b6-15cdde9dcfd4",
"type": "misc_feature"
},
{
"start": 6841,
"end": 7126,
"strand": 1,
"color": "#185e98",
"name": "4bbc",
"type": "misc_feature"
},
{
"start": 7126,
"end": 7685,
"strand": 1,
"color": "#6ff31e",
"name": "df2c",
"type": "misc_feature"
},
{
"start": 7685,
"end": 8512,
"strand": 1,
"color": "#11bf79",
"name": "89df",
"type": "misc_feature"
},
{
"start": 8512,
"end": 8660,
"strand": 1,
"color": "#7a0e05",
"name": "c96d",
"type": "misc_feature"
}
],
"customFields": {
"topology": "circular"
},
"isCircular": true
}
}
},
"molecules": [],
"reactions": []
}
|
DASi design output¶
This schema validates a json output for the DASi design |
|||||||
type |
object |
||||||
properties |
|||||||
|
type |
object |
|||||
properties |
|||||||
|
program name |
||||||
type |
string |
||||||
|
semantic version of the program |
||||||
type |
string |
||||||
|
execution trace that generated this output |
||||||
type |
object |
||||||
|
type |
array |
|||||
items |
#/definitions/molecule |
||||||
|
type |
array |
|||||
items |
#/definitions/reaction |
||||||
|
#/definitions/design_status |
||||||
definitions |
|||||||
|
This schema validates a JSON that represents a DNA/RNA sequence |
||||||
type |
object |
||||||
properties |
|||||||
|
Bases of the sequence as a string with no white spaces. |
||||||
type |
string |
||||||
|
Optional length of the sequence |
||||||
type |
integer |
||||||
|
Optional name of the sequence |
||||||
type |
string |
||||||
|
Optional id of the sequence |
||||||
type |
string |
||||||
|
Whether the topology of the sequence is circular (or linear if false) |
||||||
type |
boolean |
||||||
|
List of (optional) sequence annotations |
||||||
type |
array |
||||||
items |
#/definitions/sequenceAnnotation |
||||||
|
Optional list of custom fields on the sequence. |
||||||
type |
object |
||||||
examples |
location |
benchtop |
|||||
LIMS_ID |
UWBF_31251 |
||||||
|
Sequence annotation |
||||||
type |
object |
||||||
properties |
|||||||
|
inclusive start of the annotation |
||||||
type |
integer |
||||||
|
exclusive end of the annotation |
||||||
type |
integer |
||||||
|
color of the annotation |
||||||
type |
string |
||||||
|
type of annotation |
||||||
type |
string |
||||||
|
type |
object |
|||||
properties |
|||||||
|
name of the object |
||||||
type |
string |
||||||
|
indesx of the object |
||||||
type |
integer |
||||||
|
type of object |
||||||
type |
string |
||||||
enum |
reaction, molecule |
||||||
examples |
molecule |
||||||
reaction |
|||||||
|
#/definitions/_used_in_assemblies |
||||||
|
allOf |
#/definitions/base |
|||||
type |
object |
||||||
properties |
|||||||
|
#/definitions/sequence |
||||||
|
type |
object |
|||||
|
allOf |
#/definitions/base |
|||||
type |
object |
||||||
properties |
|||||||
|
#/definitions/_used_in_assemblies |
||||||
|
list of molecules this reaction uses as inputs (by molecule index) |
||||||
type |
array |
||||||
items |
type |
integer |
|||||
|
list of molecules this reaction uses as outputs (by molecule index) |
||||||
type |
array |
||||||
items |
type |
integer |
|||||
|
type |
array |
|||||
items |
type |
object |
|||||
properties |
|||||||
|
type |
string |
|||||
|
type |
integer |
|||||
|
Summary of the design results |
||||||
type |
object |
||||||
patternProperties |
|||||||
|
#/definitions/design_result_status |
||||||
|
type |
object |
|||||
properties |
|||||||
|
if true, then the compilation step has been run |
||||||
type |
boolean |
||||||
|
if true, then the optimization step has been run |
||||||
type |
boolean |
||||||
|
if true, then this design has at least one assembly |
||||||
type |
boolean |
||||||
|
summary of assemblies for this design |
||||||
type |
array |
||||||
items |
#/definitions/assembly_status |
||||||
|
type |
object |
|||||
properties |
|||||||
|
Cost summary for this assembly |
||||||
type |
object |
||||||
|
The index of the final assembly reaction |
||||||
type |
array |
||||||
items |
type |
integer |
|||||
|
type |
array |
|||||
items |
type |
object |
|||||
properties |
|||||||
|
type |
integer |
|||||
|
type |
object |
|||||
|
Summarized list of reactions that produce molecules used in the assembly. |
||||||
type |
array |
||||||
items |
type |
object |
|||||
properties |
|||||||
|
The start index (inclusive) of where the output molecule maps to the design |
||||||
type |
integer |
||||||
|
The end index (exclusive) of where the output molecule maps to the design |
||||||
type |
integer |
||||||
|
The type name of the reaction. |
||||||
type |
string |