Best Python code snippet using pandera_python
action.py
Source: action.py
1from entities.abstract_entity import ConceptualEntity2from entities.instrument import Instrument,Pipette3from entities.apparatus import Apparatus,Thermocycler,Centrifuge,Incubator4from entities.container import Well,Container5from property import protocols as pp6from property import actions as ap7from equivalent import abstract_equivalent as ae8from equivalent import protocol_equivalent as pe9from restriction import action_recipes as ar10class Action(ConceptualEntity):11 def __init__(self,properties=[],equivalents=[],restrictions=[]):12 if equivalents == []:13 e = [pe.ActionEquivalent()]14 else:15 e = equivalents16 p = [pp.Actions(Action),17 pp.UsesApparatus(Apparatus),18 pp.UsesInstrument(Instrument)] + properties19 super().__init__(properties=p,equivalents=e,20 restrictions=restrictions)21class Restriction(Action):22 def __init__(self,properties=[],equivalents=[],restrictions=[]):23 name = self.__class__.__name__24 e = equivalents + [ae.NameEquivalentClass(name)]25 p = properties + [pp.MayUseInstrument(default_value=Pipette),26 pp.MayUseApparatus(default_value=Thermocycler),27 pp.MayUseApparatus(default_value=Centrifuge),28 pp.MayUseApparatus(default_value=Incubator)]29 super().__init__(properties=p,equivalents=e,30 restrictions=restrictions)31class Purify(Action):32 def __init__(self,properties=[],equivalents=[],restrictions=[]):33 name = self.__class__.__name__34 e = equivalents + [ae.NameEquivalentClass(name)]35 p = properties + [pp.MayUseInstrument(default_value=Pipette),36 pp.MayUseApparatus(default_value=Centrifuge),37 pp.MayUseApparatus(default_value=Incubator)]38 super().__init__(properties=p,equivalents=e,39 restrictions=restrictions)40class Bind(Action):41 def __init__(self,properties=[],equivalents=[],restrictions=[]):42 name = self.__class__.__name__43 e = equivalents + [ae.NameEquivalentClass(name)]44 p = properties + [pp.MayUseInstrument(default_value=Pipette),45 pp.MayUseApparatus(default_value=Centrifuge)]46 super().__init__(properties=p,equivalents=e,47 restrictions=restrictions)48class Wash(Action):49 def __init__(self,properties=[],equivalents=[],restrictions=[]):50 name = self.__class__.__name__51 e = equivalents + [ae.NameEquivalentClass(name)]52 p = properties + [pp.MayUseInstrument(default_value=Pipette),53 pp.MayUseApparatus(default_value=Centrifuge)]54 super().__init__(properties=p,equivalents=e,55 restrictions=restrictions)56class Elution(Action):57 def __init__(self,properties=[],equivalents=[],restrictions=[]):58 name = self.__class__.__name__59 e = equivalents + [ae.NameEquivalentClass(name)]60 p = properties + [pp.MayUseInstrument(default_value=Pipette),61 pp.MayUseApparatus(default_value=Centrifuge),62 pp.MayUseApparatus(default_value=Incubator)]63 super().__init__(properties=p,equivalents=e,64 restrictions=restrictions)65class Transfer(Action):66 def __init__(self,properties=[],equivalents=[],restrictions=[]):67 name = [self.__class__.__name__.lower(),"dispense"]68 e = equivalents + [ae.NameEquivalentClass(name),69 pe.TransferEquivalent()]70 p = properties + [ap.Source(Well),71 ap.Destination(Well),72 ap.Volume(),73 pp.MayUseInstrument(default_value=Pipette)]74 r = restrictions + [ar.TransferRecipe()]75 super().__init__(properties=p,equivalents=e,76 restrictions=restrictions)77class Seal(Action):78 def __init__(self,properties=[],equivalents=[],restrictions=[]):79 name = self.__class__.__name__.lower()80 e = equivalents + [ae.NameEquivalentClass(name)]81 p = properties + [ap.Object(Container)]82 super().__init__(properties=p,equivalents=e,83 restrictions=restrictions)84class Unseal(Action):85 def __init__(self,properties=[],equivalents=[],restrictions=[]):86 name = self.__class__.__name__.lower()87 e = equivalents + [ae.NameEquivalentClass(name)]88 p = properties + [ap.Object(Container)]89 super().__init__(properties=p,equivalents=e,90 restrictions=restrictions)91class Spin(Action):92 def __init__(self,properties=[],equivalents=[],restrictions=[]):93 name = self.__class__.__name__.lower()94 e = equivalents + [ae.NameEquivalentClass(name)]95 p = properties + [ap.Object(Container),96 ap.Speed(),97 ap.Duration(),98 pp.MayUseApparatus(default_value=Centrifuge)]99 super().__init__(properties=p,equivalents=e,100 restrictions=restrictions)101class SeperateGel(Action):102 def __init__(self,properties=[],equivalents=[],restrictions=[]):103 name = [self.__class__.__name__.lower(),"gel_separate"]104 e = equivalents + [ae.NameEquivalentClass(name)]105 p = properties + [ap.Source(Well),106 ap.Duration(),107 ap.Volume()]108 super().__init__(properties=p,equivalents=e,109 restrictions=restrictions)110class ColonyPick(Action):111 def __init__(self,properties=[],equivalents=[],restrictions=[]):112 name = [self.__class__.__name__.lower(),"autopick"]113 e = equivalents + [ae.NameEquivalentClass(name)]114 p = properties + [ap.Source(Well),115 ap.Destination(Well)]116 super().__init__(properties=p,equivalents=e,117 restrictions=restrictions)118 119class Incubate(Action):120 def __init__(self,properties=[],equivalents=[],restrictions=[]):121 name = self.__class__.__name__.lower()122 e = equivalents + [ae.NameEquivalentClass(name)]123 p = properties + [ap.Object(Container),124 ap.Temperature(),125 ap.Duration(),126 pp.MayUseApparatus(default_value=Incubator)]127 super().__init__(properties=p,equivalents=e,128 restrictions=restrictions)129class Thermocycle(Action):130 def __init__(self,properties=[],equivalents=[],restrictions=[]):131 name = self.__class__.__name__.lower()132 e = equivalents + [ae.NameEquivalentClass(name)]133 p = properties + [ap.Object(Container),134 ap.Cycles(),135 ap.Temperature(),136 ap.Duration(),137 pp.MayUseApparatus(default_value=Thermocycler)]138 super().__init__(properties=p,equivalents=e,139 restrictions=restrictions)140class Extract(Action): # Source141 def __init__(self,properties=[],equivalents=[],restrictions=[]):142 if equivalents == []:143 e = [pe.ExtractEquivalent()]144 else:145 e = equivalents146 p = properties + [ap.Source(Well)]147 super().__init__(properties=p,equivalents=e,148 restrictions=restrictions)149class Dispense(Action): # Location150 def __init__(self,properties=[],equivalents=[],restrictions=[]):151 if equivalents == []:152 e = [pe.DispenseEquivalent()]153 else:154 e = equivalents155 p = properties + [ap.Destination(Well)]156 super().__init__(properties=p,equivalents=e,157 restrictions=restrictions)158class Consolidate(Action):159 def __init__(self,properties=[],equivalents=[],restrictions=[]):160 if equivalents == []:161 e = [pe.ConsolidateEquivalent()]162 else:163 e = equivalents164 super().__init__(properties=properties,equivalents=e,165 restrictions=restrictions)166class Distribute(Action):167 def __init__(self,properties=[],equivalents=[],restrictions=[]):168 if equivalents == []:169 e = [pe.DistributeEquivalent()]170 else:171 e = equivalents172 super().__init__(properties=properties,equivalents=e,...
genetic.py
Source: genetic.py
1from entities.abstract_entity import PhysicalEntity2from equivalent import physcial_equivalent as pe3from property.property import HasPart,HasSequence4# -------------- DNA --------------5class DNA(PhysicalEntity):6 def __init__(self,equivalents=[],properties=[]):7 if equivalents == []:8 r = [pe.DNARoleEquivalent()]9 else:10 r = equivalents11 p = properties + [HasPart(PhysicalEntity),HasSequence()]12 super().__init__(equivalents=r,properties=p)13class Promoter(DNA):14 def __init__(self,equivalents=[]):15 if equivalents == []:16 r = [pe.PromoterRoleEquivalent()]17 else:18 r = equivalents19 super().__init__(equivalents=r)20class RBS(DNA):21 def __init__(self,equivalents=[]):22 if equivalents == []:23 r = [pe.RBSRoleEquivalent()]24 else:25 r = equivalents26 super().__init__(equivalents=r)27class CDS(DNA):28 def __init__(self,equivalents=[]):29 if equivalents == []:30 r = [pe.CDSRoleEquivalent()]31 else:32 r = equivalents33 super().__init__(equivalents=r)34class Terminator(DNA):35 def __init__(self,equivalents=[]):36 if equivalents == []:37 r = [pe.TerminatorRoleEquivalent()]38 else:39 r = equivalents40 super().__init__(equivalents=r)41class Gene(DNA):42 def __init__(self,equivalents=[]):43 if equivalents == []:44 r = [pe.GeneRoleEquivalent()]45 else:46 r = equivalents47 super().__init__(equivalents=r)48class Operator(DNA):49 def __init__(self,equivalents=[]):50 if equivalents == []:51 r = [pe.OperatorRoleEquivalent()]52 else:53 r = equivalents54 super().__init__(equivalents=r)55class EngineeredRegion(DNA):56 def __init__(self,equivalents=[]):57 if equivalents == []:58 r = [pe.EngineeredRegionRoleEquivalent()]59 else:60 r = equivalents61 super().__init__(equivalents=r)62class EngineeredTag(DNA):63 def __init__(self,equivalents=[]):64 if equivalents == []:65 r = [pe.EngineeredTagRoleEquivalent()]66 else:67 r = equivalents68 super().__init__(equivalents=r)69class StartCodon(DNA):70 def __init__(self,equivalents=[]):71 if equivalents == []:72 r = [pe.StartCodonRoleEquivalent()]73 else:74 r = equivalents75 super().__init__(equivalents=r)76class Tag(DNA):77 def __init__(self,equivalents=[]):78 if equivalents == []:79 r = [pe.TagRoleEquivalent()]80 else:81 r = equivalents82 super().__init__(equivalents=r)83class NonCovBindingSite(DNA):84 def __init__(self,equivalents=[]):85 if equivalents == []:86 r = [pe.NonCovBindingSiteRoleEquivalent()]87 else:88 r = equivalents89 super().__init__(equivalents=r)90class EngineeredGene(DNA):91 def __init__(self,equivalents=[]):92 if equivalents == []:93 r = [pe.EngineeredGeneRoleEquivalent()]94 else:95 r = equivalents96 super().__init__(equivalents=r)97# -------------- Complex --------------98class Complex(PhysicalEntity):99 def __init__(self,equivalents=[]):100 if equivalents == []:101 r = [pe.ComplexRoleEquivalent()]102 else:103 r = equivalents104 super().__init__(equivalents=r)105# -------------- RNA --------------106class RNA(PhysicalEntity):107 def __init__(self,equivalents=[]):108 if equivalents == []:109 r = [pe.RNARoleEquivalent()]110 else:111 r = equivalents112 super().__init__(equivalents=r)113class mRNA(RNA):114 def __init__(self,equivalents=[]):115 if equivalents == []:116 r = [pe.mRNARoleEquivalent()]117 else:118 r = equivalents119 super().__init__(equivalents=r)120class sgRNA(RNA):121 def __init__(self,equivalents=[]):122 if equivalents == []:123 r = [pe.sgRNARoleEquivalent()]124 else:125 r = equivalents...
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