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Format DMPexcel2mat.m

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This commit is contained in:
Bryan Roessler
2024-07-25 13:12:19 -04:00
parent 4d72a078b5
commit 37533136ae
2 changed files with 133 additions and 150 deletions
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147
workflow/templates/easy/DMPexcel2mat.m
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@@ -11,12 +11,14 @@ else
end end
infile= Scanfiles(1,:); infile= Scanfiles(1,:);
cd(MPdir) cd(MPdir)
%fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector %fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
if ispc if ispc
[num, txt, raw] = xlsread(infile); %,'Yor1HitsMPsetFinal'); [num, txt, raw] = xlsread(infile); %,'Yor1HitsMPsetFinal');
fields= {txt(2,1:15)}; %or 1:17 for later but dont wish to exceed and cause error ? if used fields= {txt(2,1:15)}; %or 1:17 for later but dont wish to exceed and cause error ? if used
else else
clear MPtbl clear MPtbl
opts = detectImportOptions(infile); opts = detectImportOptions(infile);
@@ -26,16 +28,14 @@ else
MPcell= readcell(infile); MPcell= readcell(infile);
end end
cd(w) cd(w)
numb= 0; numb=0;
clear MP; clear MP;
try try
if ispc if ispc
excLnNum=3; excLnNum=3;
while (isequal(txt{excLnNum,1},'###')) while (isequal(txt{excLnNum,1},'###'))
numb=numb+1; numb=numb+1;
MP(numb).head = {raw(excLnNum,2:6)}; MP(numb).head = {raw(excLnNum,2:6)};
MP(numb).recNum = {raw((excLnNum+1):(excLnNum+384),1)}; MP(numb).recNum = {raw((excLnNum+1):(excLnNum+384),1)};
MP(numb).orf = {raw((excLnNum+1):(excLnNum+384),2)}; MP(numb).orf = {raw((excLnNum+1):(excLnNum+384),2)};
@@ -43,85 +43,76 @@ numb=numb+1;
MP(numb).genename= {raw((excLnNum+1):(excLnNum+384),12)}; MP(numb).genename= {raw((excLnNum+1):(excLnNum+384),12)};
MP(numb).drug= {raw((excLnNum+1):(excLnNum+384),8)}; MP(numb).drug= {raw((excLnNum+1):(excLnNum+384),8)};
MP(numb).media= {raw((excLnNum+1):(excLnNum+384),7)}; MP(numb).media= {raw((excLnNum+1):(excLnNum+384),7)};
if size(raw,2)>15 if size(raw,2)>15
MP(numb).orfRep= {raw((excLnNum+1):(excLnNum+384),16)}; %added 12_1005 to specify replicates Orfs in MP MP(numb).orfRep= {raw((excLnNum+1):(excLnNum+384),16)}; %added 12_1005 to specify replicates Orfs in MP
MP(numb).specifics= {raw((excLnNum+1):(excLnNum+384),17)}; %added 12_1008 to specify replicates Specific details in MP MP(numb).specifics= {raw((excLnNum+1):(excLnNum+384),17)}; %added 12_1008 to specify replicates Specific details in MP
else
MP(numb).orfRep= ' ';
MP(numb).specifics= ' ';
end
%{
if size(raw,2)>17 ; Future MP field
MP(numb).specifics2= {raw((excLnNum+1):(excLnNum+384),18)}; %added 12_1008 to specify strain Bkground in MP
else
MP(numb).specifics2= ' ';
end
%}
excLnNum=excLnNum+385;
msg=strcat('NumberOfMP = ',num2str(numb), ' lastLineNo. = ',num2str(excLnNum));
end % end if ispc
else %if not ispc
excLnNum=1;
while (isequal(MPcell{(excLnNum+2),1},'###'))
numb=numb+1;
MP(numb).head = {MPtbl(excLnNum,2:6)};
MP(numb).head{1}= table2cell(MP(numb).head{1});
MP(numb).recNum = {MPtbl((excLnNum+1):(excLnNum+384),1)};
MP(numb).recNum{1}= table2cell(MP(numb).recNum{1});
MP(numb).orf = {MPtbl((excLnNum+1):(excLnNum+384),2)};
MP(numb).orf{1}= table2cell(MP(numb).orf{1});
MP(numb).strain = {MPtbl((excLnNum+1):(excLnNum+384),3)};
MP(numb).strain{1}= table2cell(MP(numb).strain{1});
MP(numb).genename= {MPtbl((excLnNum+1):(excLnNum+384),12)};
MP(numb).genename{1}= table2cell(MP(numb).genename{1});
MP(numb).media= {MPtbl((excLnNum+1):(excLnNum+384),7)};
MP(numb).media{1}= table2cell(MP(numb).media{1});
if size(MPtbl,2)>15
MP(numb).orfRep= {MPtbl((excLnNum+1):(excLnNum+384),16)}; %added 12_1005 to specify replicates Orfs in MP
MP(numb).orfRep{1}= table2cell(MP(numb).orfRep{1});
MP(numb).specifics= {MPtbl((excLnNum+1):(excLnNum+384),17)}; %added 12_1008 to specify replicates Specific details in MP
MP(numb).specifics{1}= table2cell(MP(numb).specifics{1});
else else
MP(numb).orfRep= ' '; MP(numb).orfRep= ' ';
MP(numb).specifics= ' '; MP(numb).specifics= ' ';
end end
excLnNum=excLnNum+385; % Future MP field
msg=strcat('NumberOfMP = ',num2str(numb), 'lastLineNo. = ',num2str(excLnNum)) % if size(raw,2)>17
% MP(numb).specifics2= {raw((excLnNum+1):(excLnNum+384),18)}; %added 12_1008 to specify strain Bkground in MP
% else
% MP(numb).specifics2=' ';
% end
excLnNum=excLnNum+385;
msg=strcat('NumberOfMP = ',num2str(numb), ' lastLineNo. = ',num2str(excLnNum));
end
else
excLnNum=1;
while (isequal(MPcell{(excLnNum+2),1},'###'))
numb=numb+1;
MP(numb).head={MPtbl(excLnNum,2:6)};
MP(numb).head{1}=table2cell(MP(numb).head{1});
MP(numb).recNum={MPtbl((excLnNum+1):(excLnNum+384),1)};
MP(numb).recNum{1}=table2cell(MP(numb).recNum{1});
MP(numb).orf={MPtbl((excLnNum+1):(excLnNum+384),2)};
MP(numb).orf{1}=table2cell(MP(numb).orf{1});
MP(numb).strain={MPtbl((excLnNum+1):(excLnNum+384),3)};
MP(numb).strain{1}=table2cell(MP(numb).strain{1});
MP(numb).genename={MPtbl((excLnNum+1):(excLnNum+384),12)};
MP(numb).genename{1}= table2cell(MP(numb).genename{1});
MP(numb).media= {MPtbl((excLnNum+1):(excLnNum+384),7)};
MP(numb).media{1}= table2cell(MP(numb).media{1});
if size(MPtbl,2)>15
MP(numb).orfRep= {MPtbl((excLnNum+1):(excLnNum+384),16)}; %added 12_1005 to specify replicates Orfs in MP
MP(numb).orfRep{1}=table2cell(MP(numb).orfRep{1});
MP(numb).specifics={MPtbl((excLnNum+1):(excLnNum+384),17)}; %added 12_1008 to specify replicates Specific details in MP
MP(numb).specifics{1}=table2cell(MP(numb).specifics{1});
else
MP(numb).orfRep= ' ';
MP(numb).specifics= ' ';
end end
end %end of if ispc for MP while loop choice PC or Linux-other (ln~48) excLnNum=excLnNum+385;
msg=strcat('NumberOfMP = ',num2str(numb), 'lastLineNo. = ',num2str(excLnNum))
end
end
catch ME catch ME
h = msgbox(msg,'Check Number of Master Plates and Excel Lines') h = msgbox(msg,'Check Number of Master Plates and Excel Lines')
uiwait(h); uiwait(h);
end %end for try MP excel sheet input end %end for try MP excel sheet input
%*********************************************************************
%DMupload %DMupload
%Drug and Media Plate setup Upload from Excel %Drug and Media Plate setup Upload from Excel
%scan().plate().LocInd().gene
cd(MPdir); cd(MPdir);
excLnNum=1; excLnNum=1;
%w=pwd
%cd('D:\EASY\Experiments\'); %cd(ExpPath); %
numOfDrugs=0; numOfDrugs=0;
numOfMedias=0; numOfMedias=0;
%GUI input for selecting a MasterPlate Excel file %GUI input for selecting a MasterPlate Excel file
questdlg('\fontsize{20} Select DrugMedia File','File Selection','OK', struct('Default','OK','Interpreter','tex')); questdlg('\fontsize{20} Select DrugMedia File','File Selection','OK', struct('Default','OK','Interpreter','tex'));
[Scanfiles, pathname]=uigetfile('*.*', 'MultiSelect','off'); [Scanfiles, pathname]=uigetfile('*.*', 'MultiSelect','off');
if ispc DMdir=fullfile(pathname);
DMdir= fullfile(pathname,'\');
else
DMdir=fullfile(pathname,'/');
end
clear infile; clear infile;
infile= Scanfiles(1,:); infile= Scanfiles(1,:);
cd(DMdir) cd(DMdir)
%fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
if ispc if ispc
[num, txt, raw] = xlsread(infile); %,'Yor1HitsMPsetFinal'); [num, txt, raw] = xlsread(infile); %,'Yor1HitsMPsetFinal');
fields= {txt(2,1:5)}; fields= {txt(2,1:5)};
@@ -133,19 +124,16 @@ else
Linked= DMtbl{1,1}; Linked= DMtbl{1,1};
DMcell= readcell(infile); DMcell= readcell(infile);
end end
cd(w) cd(w)
numb=0; numb=0;
%fields= {txt(2,1:5)};
%Linked= num(1,1);
if isequal(Linked,1) %Drugs and Media are linked 1 to 1; else they are combinatorial if isequal(Linked,1) %Drugs and Media are linked 1 to 1; else they are combinatorial
clear DM; clear DM;
%try %try
excLnNum=2; excLnNum=2;
if ispc if ispc
while (~isequal(txt{excLnNum,2},'###')) while (~isequal(txt{excLnNum,2},'###'))
numb=numb+1; numb=numb+1;
DM.drug(numb) = {raw(excLnNum,2)}; DM.drug(numb) = {raw(excLnNum,2)};
DM.conc(numb) = {raw(excLnNum,3)}; DM.conc(numb) = {raw(excLnNum,3)};
@@ -156,8 +144,8 @@ while (~isequal(txt{excLnNum,2},'###'))
DM.conc2(numb) = {raw(excLnNum,8)}; DM.conc2(numb) = {raw(excLnNum,8)};
excLnNum=excLnNum+1; excLnNum=excLnNum+1;
msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), ' lastLineNo. = ',num2str(excLnNum)) msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), ' lastLineNo. = ',num2str(excLnNum))
end end
else else
clear DM clear DM
excLnNum=1; excLnNum=1;
while (~isequal(DMcell{excLnNum+1,2},'###')) while (~isequal(DMcell{excLnNum+1,2},'###'))
@@ -179,18 +167,15 @@ else
excLnNum=excLnNum+1; excLnNum=excLnNum+1;
msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), ' lastLineNo. = ',num2str(excLnNum)) msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), ' lastLineNo. = ',num2str(excLnNum))
end end
end end
end end
%Legacy contengency -Not ever used!! %Legacy contengency -Not ever used!!
if isequal(Linked,0) %0 indicates Drugs and Media are combinatorial if isequal(Linked,0) %0 indicates Drugs and Media are combinatorial
clear DM; clear DM;
excLnNum=2; excLnNum=2;
drgCnt=0; drgCnt=0;
medCnt=0; medCnt=0;
if ispc if ispc
while (~isequal(txt{excLnNum,2},'###')) while (~isequal(txt{excLnNum,2},'###'))
drgCnt=drgCnt+1; drgCnt=drgCnt+1;
DM.drug(drgCnt) = {raw(excLnNum,2)}; DM.drug(drgCnt) = {raw(excLnNum,2)};
@@ -203,7 +188,7 @@ if ispc
DM.media(medCnt) = {raw(excLnNum,4)}; DM.media(medCnt) = {raw(excLnNum,4)};
excLnNum=excLnNum+1; excLnNum=excLnNum+1;
end end
else %else if not PC (Then linux or other) else %else if not PC (Then linux or other)
excLnNum=1; excLnNum=1;
while (~isequal(DMcell{excLnNum+1,2},'###')) while (~isequal(DMcell{excLnNum+1,2},'###'))
drgCnt=drgCnt+1; drgCnt=drgCnt+1;
@@ -217,10 +202,8 @@ else %else if not PC (Then linux or other)
DM.media(medCnt) = {DMtbl(excLnNum,4)}; DM.media(medCnt) = {DMtbl(excLnNum,4)};
excLnNum=excLnNum+1; excLnNum=excLnNum+1;
end end
end end
msg=strcat('NumberOfDrugs = ',num2str(drgCnt), ' NumberOfMedias = ',num2str(medCnt) )
msg=strcat('NumberOfDrugs = ',num2str(drgCnt), ' NumberOfMedias = ',num2str(medCnt) )
end end
save (fullfile(MPdir,'MPDMmat'), 'fields','MP','DM','Linked'); save (fullfile(MPdir,'MPDMmat'), 'fields','MP','DM','Linked');