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Copy pathSwineScript.java
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423 lines (330 loc) · 29.1 KB
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package teaspoon;
import teaspoon.adaptation.FluAnalysis;
import teaspoon.adaptation.Hemagglutinin;
import teaspoon.adaptation.Neuraminidase;
import teaspoon.adaptation.WilliamsonOutputClass;
public class SwineScript {
public static void main(String[] args) {
FluAnalysis2 F = new FluAnalysis2();
int boot=10;
int output=1;
boolean printseq=true;
System.out.println("Starting Program - Gene: "+args[1]+" and Genotype: "+args[0]+"\n");
long time = System.currentTimeMillis();
if(args[1].equals("PB2") || args[1].equals("PB1") || args[1].equals("PA")){
String Name = args[1]; // specify name
String Num="#9";
if(Name.equals("PB2")){
Num = "#1"; //type
} else if(Name.equals("PB1")){
Num = "#2"; //type
} else if(Name.equals("PA")){
Num = "#3"; //type
}
String Geno = args[0]; //type
Neuraminidase Nd = new Neuraminidase();
double nr=0.1;
// create types
String[] type = {Num+Geno,Num+Geno+"a",Num+Geno+"b",Num+Geno+"c",Num+Geno+"d",Num+Geno+"e",Num+Geno+"f",Num+Geno+"g",Num+Geno+"h"};
// F.Extract("/Users/Sam/Desktop/FluData/sw_ref_PB2.fasta", "/Users/Sam/Desktop/FluData/Table.csv", "PB2",type, "1999-2000", "/Users/Sam/Desktop/out.fa");
if(Geno.equals("C1")){
// define dayes
// String[] dates={"1975","1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1998-1999-2000","2001","2002-2003","2004-2005-2006","2008-2009"};
String[] dates={"1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1998-1999-2000","2001","2002-2003","2004-2005-2006","2008-2009"};
// run to calculate neutral ratio
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Nd.badlisth1n1_NoStopCodon,0);
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Nd.badlisth1n1_NoStopCodon,0,Geno);
}
double neutralratio = F.CalcNr(woc); //save neutral ratio
// run again to get restuls with this neutral ratio
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, neutralratio,boot,Nd.badlisth1n1_NoStopCodon,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_");
} else if(Geno.equals("B1")){
// String[] dates={"1984","1991-1992-1993","1994-1995","1996-1997","1998-1999-2000","2001","2002","2003","2004","2005","2006","2007-2008","2009-2010"};
String[] dates={"1987","1991-1992-1993","1994-1995","1996-1997","1998-1999-2000","2001","2002","2003","2004","2005","2006","2007-2008","2009-2010"};
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Nd.badlisth1n1_NoStopCodon,0);
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Nd.badlisth1n1_NoStopCodon,0,Geno);
}
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, neutralratio,boot,Nd.badlisth1n1_NoStopCodon,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_");
} else if(Geno.equals("T1")){
String[] dates={"1999","2000-2001-2003","2003","2004","2005","2006","2007","2008","2009-2010"};
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Nd.badlisth1n1_NoStopCodon,0);
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Nd.badlisth1n1_NoStopCodon,0,Geno);
}
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, neutralratio,boot,Nd.badlisth1n1_NoStopCodon,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_");
}
}
//********************/********************/********************/********************/********************/********************/********************/********************
//HA HA1 HA2 teaspoon.adaptation.Split
if(args[1].equals("H1")){
String Name = args[1]; // specify name
String Num = "#4"; //type
String Geno = args[0]; //type
int A=10;
Hemagglutinin Hd = new Hemagglutinin(); /// important needed to change lists
// create types
String[] type = {Num+Geno,Num+Geno+"a",Num+Geno+"b",Num+Geno+"c",Num+Geno+"d",Num+Geno+"e",Num+Geno+"f",Num+Geno+"g",Num+Geno+"h"};
if(args[0].equals("B1")){
String[] dates ={"1987","1991-1992-1993","1994-1995-1996","1997-1998-1999","2000-2001-2002","2003-2004","2005","2006-2007","2008","2009-2010"}; //ea
// String[] dates ={"1991-1992-1993","1994-1995-1996","1997-1998-1999","2000-2001-2002","2003-2004","2005","2006-2007","2008","2009-2010"}; //ea
double nr = 0.1; // EA
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Hd.HAH1,0);
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, neutralratio,boot,Hd.HAH1,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HA2"+"_");
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Hd.HAH1,0,"B1_HA2");
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Hd.HAH1,1,"B1_HA1");
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Hd.HAH1,0,"B1_HA");
}
WilliamsonOutputClass woc3 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, neutralratio,boot,Hd.HAH1,0);
F.print(woc3, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HA"+"_");
WilliamsonOutputClass woc4 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, neutralratio,boot,Hd.HAH1,1);
F.print(woc4, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HA1"+"_");
// String[] dateswa ={"1979","1980-1981-1982-1983","1984-1985-1986-1987","1990-1991-1992-1993","1994-1995-1996","1997-1998-1999","2000-2001-2002","2003-2004","2005","2006-2007","2008","2009-2010"}; //eawa
// String[] dateswa ={"1980-1981-1982-1983","1984-1985-1986-1987","1990-1991-1992-1993","1994-1995-1996","1997-1998-1999","2000-2001-2002","2003-2004","2005","2006-2007","2008","2009-2010"}; //eawa
// teaspoon.adaptation.WilliamsonOutputClass woc5 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+"_wa.fasta", "/Users/Sam/Desktop/FluData/Table_H1.csv",Name, type,dateswa,0, -2, neutralratio,boot,Hd.HAH1,1);
// F.print(woc5, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HA1_With Additions"+"_");
} else if(args[0].equals("C1")){
// String[] dates ={"1975","1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1999","2000","2001","2002","2003","2004","2005","2006-2007","2008","2009-2010"}; //cs
String[] dates ={"1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1999-2000","2001","2002","2003","2004","2005","2006-2007","2008","2009-2010"}; //cs
double nr = 0.1; // EA
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Hd.HAH1,0);
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, neutralratio,boot,Hd.HAH1,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HA2"+"_");
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Hd.HAH1,0,"C1_HA2");
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Hd.HAH1,1,"C1_HA1");
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Hd.HAH1,0,"C1_HA");
}
WilliamsonOutputClass woc3 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, neutralratio,boot,Hd.HAH1,0);
F.print(woc3, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HA"+"_");
WilliamsonOutputClass woc4 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, neutralratio,boot,Hd.HAH1,1);
F.print(woc4, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HA1"+"_");
}
}
//********************/********************/********************/********************/********************/********************/********************/********************
//HA surface internal split
if(args[1].equals("H1si")){
String Name = "H1"; // specify name
String Num = "#4"; //type
String Geno = args[0]; //type
int A=10;
Hemagglutinin Hd = new Hemagglutinin(); /// important needed to change lists
// create types
String[] type = {Num+Geno,Num+Geno+"a",Num+Geno+"b",Num+Geno+"c",Num+Geno+"d",Num+Geno+"e",Num+Geno+"f",Num+Geno+"g",Num+Geno+"h"};
// String[] type = {Num+Geno,Num+Geno+"a"};
if(args[0].equals("B1")){
// String[] dates ={"1984","1991-1992-1993","1994-1995-1996","1997-1998-1999","2000-2001-2002","2003-2004","2005","2006-2007","2008","2009-2010"}; //ea
String[] dates ={"1987","1991-1992-1993","1994-1995-1996","1997-1998-1999","2000-2001-2002","2003-2004","2005","2006-2007","2008","2009-2010"}; //ea
// String[] dates ={"1991-1992-1993","1994-1995-1996","1997-1998-1999","2000-2001-2002","2003-2004","2005","2006-2007","2008","2009-2010"}; //ea
double nr = 0.1; // EA
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Hd.H1,0);
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, neutralratio,boot,Hd.H1,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HAi"+"_");
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Hd.H1,0,"B1_HAi");
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Hd.H1,1,"B1_HAs");
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Hd.H1,0,"B1_HA");
}
WilliamsonOutputClass woc3 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, neutralratio,boot,Hd.H1,0);
F.print(woc3, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HAsi"+"_");
WilliamsonOutputClass woc4 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, neutralratio,boot,Hd.H1,1);
F.print(woc4, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HAs"+"_");
// String[] dateswa ={"1979","1980-1981-1982-1983","1984-1985-1986-1987","1990-1991-1992-1993","1994-1995-1996","1997-1998-1999","2000-2001-2002","2003-2004","2005","2006-2007","2008","2009-2010"}; //eawa
// String[] dateswa ={"1980-1981-1982-1983","1984-1985-1986-1987","1990-1991-1992-1993","1994-1995-1996","1997-1998-1999","2000-2001-2002","2003-2004","2005","2006-2007","2008","2009-2010"}; //eawa
// teaspoon.adaptation.WilliamsonOutputClass woc5 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+"_wa.fasta", "/Users/Sam/Desktop/FluData/Table_H1.csv",Name, type,dateswa,0, -2, neutralratio,boot,Hd.H1,1);
// F.print(woc5, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HAs_With Additions"+"_");
} else if(args[0].equals("C1")){
// String[] dates ={"1975","1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1999","2000","2001","2002","2003","2004","2005","2006-2007","2008","2009-2010"}; //cs
String[] dates ={"1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1999","2000","2001","2002","2003","2004","2005","2006-2007","2008","2009-2010"}; //cs
double nr = 0.1; // EA
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Hd.H1,0);
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, neutralratio,boot,Hd.H1,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HAi"+"_");
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Hd.H1,0,"C1_HAi");
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Hd.H1,1,"C1_HAs");
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Hd.H1,0,"C1_HA");
}
WilliamsonOutputClass woc3 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, neutralratio,boot,Hd.H1,0);
F.print(woc3, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HAsi"+"_");
WilliamsonOutputClass woc4 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, neutralratio,boot,Hd.H1,1);
F.print(woc4, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_HAs"+"_");
}
}
//********************/********************/********************/********************/********************/********************/********************/********************
if(args[1].equals("NP")){
//NP
String Name = args[1]; // specify name
String Num = "#5"; //type
String Geno = args[0]; //type
Neuraminidase Nd = new Neuraminidase();
// create types
String[] type = {Num+Geno,Num+Geno+"a",Num+Geno+"b",Num+Geno+"c",Num+Geno+"d",Num+Geno+"e",Num+Geno+"f",Num+Geno+"g",Num+Geno+"h"};
double nr=0.1;
if(args[0].equals("B1")){
// String[] dates ={"1984","1991-1992-1993","1994-1995-1996","1997-1998","1999","2000-2001","2002","2003","2004","2005","2006","2007","2008","2009-2010"};
String[] dates ={"1987","1991-1992-1993","1994-1995-1996","1997-1998","1999","2000-2001","2002","2003","2004","2005","2006","2007","2008","2009-2010"};
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table_NP.csv",Name, type,dates,0, -1, nr,1,Nd.badlisth1n1_NoStopCodon,0);
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table_NP.csv",Name, type,dates,0, -1, neutralratio,boot,Nd.badlisth1n1_NoStopCodon,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_");
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Nd.badlisth1n1_NoStopCodon,0,Geno);
}
}else if(args[0].equals("C1")){
// String[] dates ={"1975","1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1999","2000","2001","2002","2003","2004","2005","2006","2007","2008","2009-2010"};
String[] dates ={"1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1999","2000","2001","2002","2003","2004","2005","2006","2007","2008","2009-2010"};
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table_NP.csv",Name, type,dates,0, -1, nr,1,Nd.badlisth1n1_NoStopCodon,0);
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table_NP.csv",Name, type,dates,0, -1, neutralratio,boot,Nd.badlisth1n1_NoStopCodon,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_");
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Nd.badlisth1n1_NoStopCodon,0,Geno);
}
}
}
//********************/********************/********************/********************/********************/********************/********************/********************
if(args[1].equals("N1")){
String Name = args[1]; // specify name
String Num = "#6"; //type
String Geno = args[0]; //type
Neuraminidase Nd = new Neuraminidase();
// create types
String[] type = {Num+Geno,Num+Geno+"a",Num+Geno+"b",Num+Geno+"c",Num+Geno+"d",Num+Geno+"e",Num+Geno+"f",Num+Geno+"g",Num+Geno+"h"};
if(args[0].equals("B1")){
// String[] dates = {"1984","1991-1992-1993","1994-1995-1996","1997-1998-1999","2000-2001","2002-2003","2004","2005","2006-2007","2008","2009"};
String[] dates = {"1987","1991-1992-1993","1994-1995-1996","1997-1998-1999","2000-2001","2002-2003","2004","2005","2006-2007","2008","2009"};
double nr = 0.1; // EA
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Nd.badlisth1n1_NoStopCodon,0);
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, neutralratio,boot,Nd.badlisth1n1_NoStopCodon,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_NAi"+"_");
WilliamsonOutputClass woc3 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, neutralratio,boot,Nd.badlisth1n1_NoStopCodon,0);
F.print(woc3, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_NA"+"_");
WilliamsonOutputClass woc4 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, neutralratio,boot,Nd.badlisth1n1_NoStopCodon,1);
F.print(woc4, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_NAs"+"_");
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Nd.badlisth1n1_NoStopCodon,0,"B1_NAi");
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Nd.badlisth1n1_NoStopCodon,1,"B1_NAs");
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Nd.badlisth1n1_NoStopCodon,0,"B1_NA");
}
}else if(args[0].equals("C1")){
// String[] dates = {"1975","1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1999-2000","2001","2002-2003","2004-2005","2006-2007","2008-2009"};
String[] dates = {"1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1999-2000","2001","2002-2003","2004-2005","2006-2007","2008-2009"};
double nr = 0.1; // EA
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Nd.badlisth1n1_NoStopCodon,0);
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, neutralratio,boot,Nd.badlisth1n1_NoStopCodon,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_NAi"+"_");
WilliamsonOutputClass woc3 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, neutralratio,boot,Nd.badlisth1n1_NoStopCodon,0);
F.print(woc3, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_NA"+"_");
WilliamsonOutputClass woc4 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, neutralratio,boot,Nd.badlisth1n1_NoStopCodon,1);
F.print(woc4, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_NAs"+"_");
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Nd.badlisth1n1_NoStopCodon,0,"C1_NAi");
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -2, nr,1,Nd.badlisth1n1_NoStopCodon,1,"C1_NAs");
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Nd.badlisth1n1_NoStopCodon,0,"C1_NA");
}
}
}
//********************/********************/********************/********************/********************/********************/********************/********************
if(args[1].equals("M1") || args[1].equals("M2") ){
//M1 M2
String Name = args[1]; // specify name
String Num = "#7"; //type
String Geno = args[0]; //type
Hemagglutinin Hd = new Hemagglutinin();
// create types
String[] type = {Num+Geno,Num+Geno+"a",Num+Geno+"b",Num+Geno+"c",Num+Geno+"d",Num+Geno+"e",Num+Geno+"f",Num+Geno+"g",Num+Geno+"h"};
double nr=0.1;
if(args[0].equals("C1")){
// String[] dates ={"1975","1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1999-2000","2001","2002","2003","2004","2005","2006","2007","2008","2009-2010"};
String[] dates ={"1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1999-2000","2001","2002","2003","2004","2005","2006","2007","2008","2009-2010"};
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table_MP.csv",Name, type,dates,0, -1, nr,1,Hd.HA,0);
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table_MP.csv",Name, type,dates,0, -1, neutralratio,boot,Hd.HA,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_");
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Hd.HA,0,Geno);
}
}else if(args[0].equals("B1")){
// String[] dates ={"1984","1991-1992-1993","1994-1995-1996","1997-1998","1999","2000-2001","2002","2003","2004","2005","2006","2007","2008","2009-2010"};
String[] dates ={"1987","1991-1992-1993","1994-1995-1996","1997-1998","1999","2000-2001","2002","2003","2004","2005","2006","2007","2008","2009-2010"};
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table_MP.csv",Name, type,dates,0, -1, nr,1,Hd.HA,0);
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table_MP.csv",Name, type,dates,0, -1, neutralratio,boot,Hd.HA,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_");
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Hd.HA,0,Geno);
}
}
}
//********************/********************/********************/********************/********************/********************/********************/********************
if(args[1].equals("NS1") || args[1].equals("NS2") ){
//M1 M2
String Name = args[1]; // specify name
String Num = "#8"; //type
String Geno = args[0]; //type
Hemagglutinin Hd = new Hemagglutinin();
// create types
String[] type = {Num+Geno,Num+Geno+"a",Num+Geno+"b",Num+Geno+"c",Num+Geno+"d",Num+Geno+"e",Num+Geno+"f",Num+Geno+"g",Num+Geno+"h"};
double nr=0.1;
if(args[0].equals("C1")){
// String[] dates ={"1975","1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1998-1999","2000","2001","2002","2003","2004","2005","2006","2007","2008","2009-2010"};
String[] dates ={"1976","1977","1978","1979","1980-1981","1985-1986-1987","1988-1990-1991","1993","1994","1998-1999","2000","2001","2002","2003","2004","2005","2006","2007","2008","2009-2010"};
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table_NS.csv",Name, type,dates,0, -1, nr,1,Hd.HA,0);
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table_NS.csv",Name, type,dates,0, -1, neutralratio,boot,Hd.HA,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_");
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Hd.HA,0,Geno);
}
}else if(args[0].equals("B1")){
// String[] dates ={"1984","1991-1992-1993","1994-1995-1996","1997-1998","1999","2000","2001","2002","2003","2004","2005","2006","2007","2008","2009-2010"};
String[] dates ={"1987","1991-1992-1993","1994-1995-1996","1997-1998","1999","2000","2001","2002","2003","2004","2005","2006","2007","2008","2009-2010"};
WilliamsonOutputClass woc = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table_NS.csv",Name, type,dates,0, -1, nr,1,Hd.HA,0);
double neutralratio = F.CalcNr(woc);
WilliamsonOutputClass woc2 = F.RunnerBS("/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table_NS.csv",Name, type,dates,0, -1, neutralratio,boot,Hd.HA,0);
F.print(woc2, output,"/Users/Sam/Desktop/out/"+Name+"_"+Geno+"_");
if(printseq){
F.WriteSequencesGeno("/Users/Sam/Desktop/out2/Swine","/Users/Sam/Desktop/FluData/sw_ref_"+Name+".fasta", "/Users/Sam/Desktop/FluData/Table.csv",Name, type,dates,0, -1, nr,1,Hd.HA,0,Geno);
}
}
}
//********************/********************/********************/********************/********************/********************/********************/********************
if(args[1].equals("H1N1") || args[1].equals("H3N2") ){
FluAnalysis ff = new FluAnalysis();
double[] nr = {0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1};
String[] names = {"PB2","PB1","PA","HAsi","HAs","HAi","HA","HA1","HA2","NP","NA","NAs","NAi","M1","M2","NS1"};
WilliamsonOutputClass[] woc = ff.HumanRunner(1, nr,args[1]);
int k=0;
for(WilliamsonOutputClass i :woc){
nr[k]=F.CalcNr(i);
k++;
}
nr[3]=nr[5];nr[4]=nr[5];
nr[6]=nr[8];nr[7]=nr[8];
nr[10]=nr[12];nr[11]=nr[12];
WilliamsonOutputClass[] woc2 = ff.HumanRunner(boot, nr,args[1]);
k=0;
for(WilliamsonOutputClass i :woc2){
F.print(i, output, "/Users/Sam/Desktop/out/"+names[k]+"_"+args[1]+"_");
k++;
}
}
time = System.currentTimeMillis() - time;
System.out.println("Program - Gene: "+args[1]+" and Genotype: "+args[0]+" took "+ time/1000 + " seconds");
}
}