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DOCUMENTATION

This document describes the syntax and semantics of the class used ingenerating the sequencing graph from an input assay file.

1. Class : SequencingGraph

This class reads an input assay file in text format and identifies the modulesand reagents in the assay. It also checks for the syntax and semantics of theinput assay file and generates a directed sequencing graph from the assay fileusing the networkX tool.

1.1 Input : An assay file where the sequence of instructions are expressedusing an instruction set described below :

1.1.1 Structure of the input file :

Instruction Set :

Primitives Syntax Description

DISPENSER DISPENSER(Dispenserid, Reagent Name)

This primitive indicatesa dispenser module withits identifier and thereagent in it.

MIX MIX(Mixing id,Source_1, Source_2,Time_Unit)

This primitive indicatesa mixer module with thefirst argument being themodule identifier and

the second and thirdarguments are the sourcemodules for mixer andthe last argument is theamount of timerequired.

DETECT DETECT(Detection id, This primitive indicates

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Source, Time_Unit) an optical detectionmodule where moduleidentifier and the sourcemodule for the droplet tobe detected and thedetection time arespecified as arguments,respectively

HEAT HEAT(Heater id,Source, Time_Unit)

This primitive indicatesa heater module wheremodule identifier andthe source module forthe droplet to be heatedand the heating durationare specified asarguments.

OUTPUT OUTPUT(Output id,Source)

This indicates an outputmodule with moduleidentifier and the sourcemodule from whichdroplet will come to theoutput module.

1.2 Description of the class SequencingGraph :

1.2.1 Private variables :

Identifier Description

_listOfIds Stores the module identifiers

_listOfReagents Stores the list of reagents indispenser modules

_assayFileFP File object for reading the input assayfile

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_tokenStream Tokens are read into this list from theinput assay file

NOTE

The public variable seqGraph stores a DiGraph object which is thesequencing graph generated from the input assay file.

1.2.2 METHODS

Name of Method Description

__getNextToken Returns the next token from thestream of tokens

__genSequencingGraph Calls different methods for validationof the input assay file

__validateDispense Checks the syntax for dispenseoperations

__validateMix Checks the syntax for mixingoperations

__validateOutput Checks the syntax for outputoperations

__validateHeat Checks the syntax for heatingoperations

__validateDetect Checks the syntax for detectionoperations

printSequencingGraph Outputs the sequencing graph in .dotfile