%% INPUTS
clear
clc
warning('off', 'Bioinfo:oligoprop:SeqLengthTooShort');

file1 = fopen('genetext.txt');
file2 = fopen('output.txt','w');
file3 = fopen('fastaoutput','w');
gene = textscan(file1, '%s');
sequence= char(gene{1})
sequencei= sequence(34:(length(sequence)-33));
h=basecount(sequencei);
b=h.A+h.G+h.C+h.T;
bp=b;
Illumniaforward=('gttcagagttctacagtccgacgatc');
Illumniareverse=('ccttggcacccgagaattcca');
labels={'Forward and Reverse ' 'Section '}
labelnumber={1:35}
%% Choses the amount and how long of primers

codons=bp/3;
primers=codons/42;
ap = ceil(primers);
avgcodon = floor(codons/ap);
pl=avgcodon*(ones(1,ap));
remainder=round((ap*(abs(avgcodon-(codons/ap)))));
for i=1:remainder;
    pl(i)=pl(i)+1;
end
pl=pl*3
p=pl;
for k=2:length(pl);
    p(k)=pl(k)+p(k-1);
end
% initial division of the sequence
P=cell(length(pl),1);
P{1}=sequencei(1:(pl(1)));
for j=2:length(p)
    P{j}=sequencei((p(j-1)+1):(p(j)));
end

%{Creation of the L, B, and SECTION variable. L will be the leading sections
%for each of the primers while the B is the lagging and PRIMER is the
%finally assembled primers.
leadingsection=sequence(1:33);
Lag=cell(length(pl),1);
Lead=cell(length(pl),1);
L=cell(length(pl),1);
B=cell(length(pl),1);
SECTION=cell(length(pl),1);
FORWARDPRIMER=cell(length(pl),1);
REVERSEPRIMER=cell(length(pl),1);
%Creat the Lead and Lag so that the later code can sort through them and
%make the best primers based on the melting temperatures
Lead{1}=sequence(1:33);
Lag{end}=seqrcomplement(sequence((length(sequence)-32):length(sequence)));
for index = 2:length(pl);
    Lead{index}=P{index-1}((length(P{index-1})-33):(length(P{index-1})));
    Lag{index-1}=seqrcomplement(P{index}(1:33));
end

IFN=0
%Need to create the the first leading section out of the preliminary "junk
%base pairs.  The code will create all the possible leading sections, check
%the mealting point and then choose the closest to the set point of 55C.
%It will then move on and check the lagging section of the primer and see
%if they are close in temp, if they are not it will choose a new leading
%and lagging section that are closer.
leadtestsec=cell(length(pl),33);
lagtestsec=cell(length(pl),33);
for index = 1:length(pl);
    
    for jindex = 1:33;
        leadtestsec{index,jindex}=Lead{index}((34-jindex):33);
        propslead=oligoprop(leadtestsec{index,jindex});
        TMlead(jindex)=propslead.Tm(5)+6;
        
        lagtestsec{index,jindex}=(Lag{index}(34-jindex:33));
        propslag=oligoprop(lagtestsec{index,jindex});
        TMlag(jindex)=propslag.Tm(5)+6;
        
    end
    TMdifflead=abs(TMlead-55);
    TMdifflag=abs(TMlag-55);
    winnerleadindex=find(TMdifflead==min(TMdifflead));
    winnerlagindex= find(TMdifflag==min(TMdifflag));
    TMwinnerlag(index) = TMlag(winnerlagindex);
    TMwinnerlead(index) = TMlead(winnerleadindex);
    
    
    if TMwinnerlag(index) > TMwinnerlead(index)+2 || TMwinnerlag(index) < TMwinnerlead(index)-2
        IFN=IFN+1
        if abs(TMwinnerlag(index)-55)<abs(TMwinnerlead(index)-55)
            TMdifflead=abs(TMlead-TMlag(winnerlagindex));
            winnerleadindex=find(TMdifflead==min(TMdifflead));
        else
            TMdifflag=abs(TMlag-TMlead(winnerleadindex));
            winnerlagindex=find(TMdifflag==min(TMdifflag));
        end
        TMwinnerlag(index) = TMlag(winnerlagindex);
        TMwinnerlead(index) = TMlead(winnerleadindex);
        
    end
    L{index}=leadtestsec{index,winnerleadindex};
    B{index}=lagtestsec{index,winnerlagindex};
end

for m=1:length(pl);
    FORWARDPRIMER{m}(1:26)=Illumniaforward;
    FORWARDPRIMER{m}(27:(26+length(L{m})))=L{m};
    REVERSEPRIMER{m}(1:21)=Illumniareverse;
    REVERSEPRIMER{m}(22:(21+length(B{m})))=B{m};
    
end
for q=1:length(p);
    SECTION{q}(1:length(L{q}))=L{q};
    SECTION{q}((length(L{q})+1):(length(L{q})+length(P{q})))=P{q};
    SECTION{q}((length(L{q})+length(P{q})+1):((length(L{q})+length(P{q}))+length(B{q})))=seqrcomplement(B{q});
    fprintf(file2,'%s',labels{1})
    fprintf(file2,'%d\n',labelnumber{1}(q));
    fprintf(file2,'%s\n%s;\n',FORWARDPRIMER{q}(1:end),REVERSEPRIMER{q}(1:end),TMwinnerlead(q),TMwinnerlag(q));
end
for n=1:length(p);
    fprintf(file2,'%s',labels{2})
    fprintf(file2,'%d\n',labelnumber{1}(n));
    fprintf(file2,'%s\n%s;\n',SECTION{n})
    fastawrite('fasta.txt',labels{2},SECTION{n})
end
%output to text files


fclose(file1);
fclose(file2);
fclose(file3);