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DMPexcel2mat.m refactor

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Bryan Roessler
2024-07-27 01:05:05 -04:00
parent 174f5e7463
commit 2202b81777
1 changed files with 167 additions and 60 deletions
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227
workflow/templates/easy/DMPexcel2mat.m
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@@ -1,34 +1,100 @@
%% CALLED BY EASYconsole.m %%
w=pwd
numOfMPs=0;
%GUI input for selecting a MasterPlate Excel file
questdlg('\fontsize{20} Select Master Plate File','File Selection','OK', struct('Default','OK','Interpreter','tex'))
[Scanfiles, pathname]=uigetfile('*.*','MultiSelect','off');
if ispc
MPdir= fullfile(pathname,'\');
else
MPdir=fullfile(pathname,'/');
global mpdmFile
global masterPlateFile
global drugMediaFile
global matDir
% If we already have mpdmFile, don't recreate
if exist(mpdmFile, 'file') && ~isempty(mpdmFile)
disp(strcat('The Drug Media/MasterPlate Annotation File: ', mpdmFile, ' exists, skipping DMPexcel2mat.m'));
return
end
infile= Scanfiles(1,:);
% Do our best to find and load a relevant MasterPlate file
if ~exist(masterPlateFile, 'file') || isempty(masterPlateFile)
if exist(fullfile(matDir), 'dir')
% Try to find the masterPlateFile automatically (newest created first)
try
files=dir(matDir)
mpFiles={files(strncmp(files.name, 'MasterPlate_', 12)).name};
isempty(mpFiles) && throw(MException('MATLAB:dir', 'No MasterPlate_ files in the default MasterPlate directory'));
% this sorts by date (newest first)
[~, sortedIndices]=sort(datenum({files(strncmp(mpFiles.name, 'MasterPlate_', 12)).date}), 'descend');
sortedFiles=mpFiles(sortedIndices);
masterPlateFile=sortedFiles{1};
disp('Using newest MasterPlate file: ', masterPlateFile, ', skipping directory selection');
catch Me
% This can be silent, not really an error
end
cd(MPdir)
%fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
for i-1:5 % give users 5 chances to get it right
try
% For standalone mode
% GUI input for selecting a MasterPlate Excel file
questdlg('Select MasterPlate Directory (containing DrugMedia_ & MasterPlate_ files)','Directory Selection','OK',...
struct('Default','OK','Interpreter','tex'))
dirToScan=uigetdir();
files=dir(dirToScan);
mpFiles={files(strncmp(files.name, 'MasterPlate_', 12)).name};
isempty(mpFiles) && throw(MException('MATLAB:dir', 'No MasterPlate_ files in directory'))
% this sorts by date (newest first)
[~, sortedIndices]=sort(datenum({files(strncmp(mpFiles.name, 'MasterPlate_', 12)).date}), 'descend');
sortedFiles=mpFiles{sortedIndices};
masterPlateFile=sortedFiles{1};
disp('Using newest MasterPlate file: ', masterPlateFile, ', skipping directory selection');
break
catch ME
h = msgbox(ME.message, 'Error', 'error');
disp('Rerunning directory selection');
% I don't know what else we'll need to do here
end
end
else
for i-1:5 % give users 5 chances to get it right
try
% For standalone mode
% GUI input for selecting a MasterPlate Excel file
questdlg('Select MasterPlate Directory (containing DrugMedia_ & MasterPlate_ files)','Directory Selection','OK',...
struct('Default','OK','Interpreter','tex'))
dirToScan=uigetdir();
files=dir(dirToScan);
mpFiles={files(strncmp(files.name, 'MasterPlate_', 12)).name};
isempty(mpFiles) && throw (MException('MATLAB:dir', 'No MasterPlate_ files in directory'))
% this sorts by date (newest first)
[~, sortedIndices]=sort(datenum({files(strncmp(mpFiles.name, 'MasterPlate_', 12)).date}), 'descend');
sortedFiles=mpFiles{sortedIndices};
masterPlateFile=sortedFiles{1};
disp('Using newest MasterPlate file: ', masterPlateFile, ', skipping directory selection');
break
catch ME
h = msgbox(ME.message, 'Error', 'error');
uiwait(h);
disp('Rerunning directory selection');
% I don't know what else we'll need to do here
end
end
end
else
disp(strcat('Using MasterPlate file: ', masterPlateFile, ', skipping directory selection');
end
% fid=fopen(masterPlateFile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
% TODO needs explanation, it isn't clear what it is for
% The input files should be csv, not xlsx
% This whole file could be much better and more portable
if ispc
[num, txt, raw] = xlsread(infile); %,'Yor1HitsMPsetFinal');
[num, txt, raw] = xlsread(masterPlateFile); %,'Yor1HitsMPsetFinal');
fields= {txt(2,1:15)}; %or 1:17 for later but dont wish to exceed and cause error ? if used
else
clear MPtbl
opts = detectImportOptions(infile);
MPtbl = readtable(infile,opts);
MPtbl= readtable(infile);
fields= {opts.VariableNames}; %? if used anywhere although 'saved' to MPDMmat
MPcell= readcell(infile);
opts=detectImportOptions(masterPlateFile);
MPtbl=readtable(masterPlateFile,opts);
MPtbl=readtable(masterPlateFile);
fields={opts.VariableNames}; %? if used anywhere although 'saved' to MPDMmat
MPcell=readcell(masterPlateFile);
end
cd(w)
numb=0;
clear MP;
try
@@ -44,24 +110,20 @@ try
MP(numb).drug= {raw((excLnNum+1):(excLnNum+384),8)};
MP(numb).media= {raw((excLnNum+1):(excLnNum+384),7)};
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).specifics= {raw((excLnNum+1):(excLnNum+384),17)}; %added 12_1008 to specify replicates Specific details 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
else
MP(numb).orfRep= ' ';
MP(numb).specifics= ' ';
end
% Future MP field
% if size(raw,2)>17
% MP(numb).specifics2= {raw((excLnNum+1):(excLnNum+384),18)}; %added 12_1008 to specify strain Bkground in MP
% 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;
@@ -80,57 +142,104 @@ try
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= {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={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
excLnNum=excLnNum+385;
msg=strcat('NumberOfMP = ',num2str(numb), 'lastLineNo. = ',num2str(excLnNum))
end
end
catch ME
h = msgbox(msg,'Check Number of Master Plates and Excel Lines')
h = msgbox(ME.message, 'Error', 'error');
uiwait(h);
end %end for try MP excel sheet input
end
%DMupload
%Drug and Media Plate setup Upload from Excel
cd(MPdir);
excLnNum=1;
numOfDrugs=0;
numOfMedias=0;
%GUI input for selecting a MasterPlate Excel file
questdlg('\fontsize{20} Select DrugMedia File','File Selection','OK', struct('Default','OK','Interpreter','tex'));
[Scanfiles, pathname]=uigetfile('*.*', 'MultiSelect','off');
DMdir=fullfile(pathname);
clear infile;
infile= Scanfiles(1,:);
cd(DMdir)
% Grabbing the bare filename from the MasterPlate file to see if we can automatically
% find a matching DrugMedia file
[mpFile, mpPath]=masterPlateFile
mpFileParts=strsplit(mpFile, '_');
mpBareFileName=strjoin(parts(2:end-1), '_');
if ispc
[num, txt, raw] = xlsread(infile); %,'Yor1HitsMPsetFinal');
fields= {txt(2,1:5)};
Linked= num(1,1);
if ~exist(drugMediaFile, 'file') || isempty(drugMediaFile)
if exist(fullfile(matDir), 'dir')
try
dmFileToTest=fullfile(mpPath, 'DrugMedia_', mpBareFileName, '.xlsx');
if exist(dmFileToTest, 'file') % Try to find a matching drug media file
drugMediaFile=dmFileToTest;
disp(strcat('Using matching DrugMedia file: ', drugMediaFile, ', skipping directory selection'));
else
% Try to find the DrugMedia file automatically (newest created first)
files=dir(matDir)
dmFiles={files(strncmp(files.name, 'DrugMedia_', 10)).name};
isempty(dmFiles) && throw (MException('MATLAB:dir', 'No DrugMedia_ files in directory'))
% this sorts by date (newest first)
[~, sortedIndices]=sort(datenum({files(strncmp(dmFiles.name, 'DrugMedia_', 10)).date}), 'descend');
sortedFiles=dmFiles{sortedIndices};
drugMediaFile=sortedFiles{1};
disp(strcat('Using newest DrugMedia file: ', drugMediaFile, ', skipping directory selection'));
end
catch Me
% This can be silent, not really an error
end
else
for i-1:5 % give users 5 chances to get it right
try
% GUI input for selecting a DrugMedia file
% sort by newest matching DrugMedia file and return that if we find one
% For standalone mode
% GUI input for selecting a MasterPlate Excel file
questdlg('Select DrugMedia directory','Directory Selection','OK',...
struct('Default','OK','Interpreter','tex'))
dirToScan=uigetdir();
files=dir(dirToScan)
dmFiles={files(strncmp(files.name, 'DrugMedia_', 10)).name};
isempty(dmFiles) && throw (MException('MATLAB:dir', 'No DrugMedia_ files in directory'))
% this sorts by date (newest first)
[~, sortedIndices]=sort(datenum({files(strncmp(dmFiles.name, 'DrugMedia_', 10)).date}), 'descend');
sortedFiles=dmFiles{sortedIndices};
drugMediaFile=sortedFiles{1};
catch ME
h = msgbox(ME.message, 'Error', 'error');
uiwait(h);
disp('Rerunning directory selection')
% I don't know what else we'll need to do here
end
end
end
end
else
opts = detectImportOptions(infile);
DMtbl= readtable(infile,opts);
fields= opts.VariableOptions;
Linked= DMtbl{1,1};
DMcell= readcell(infile);
disp(strcat('Using drugMediaFile: ', drugMediaFile, ', skipping directory selection'));
end
cd(w)
numb=0;
% Drug and Media Plate setup
% TODO needs better explanation
if ispc
[num, txt, raw]=xlsread(drugMediaFile); %'Yor1HitsMPsetFinal');
fields={txt(2,1:5)};
Linked=num(1,1);
else
opts=detectImportOptions(drugMediaFile);
DMtbl=readtable(drugMediaFile,opts);
fields=opts.VariableOptions;
Linked=DMtbl{1,1};
DMcell=readcell(drugMediaFile);
end
if isequal(Linked,1) %Drugs and Media are linked 1 to 1; else they are combinatorial
% TODO needs better explanation
numb=0;
if isequal(Linked,1) % Drugs and Media are linked 1 to 1; else they are combinatorial
clear DM;
%try
excLnNum=2;
if ispc
while (~isequal(txt{excLnNum,2},'###'))
@@ -169,8 +278,8 @@ if isequal(Linked,1) %Drugs and Media are linked 1 to 1; else they are combina
end
end
end
%Legacy contengency -Not ever used!!
if isequal(Linked,0) %0 indicates Drugs and Media are combinatorial
% Legacy contengency: not ever used
if isequal(Linked,0) % 0 indicates Drugs and Media are combinatorial
clear DM;
excLnNum=2;
drgCnt=0;
@@ -188,7 +297,7 @@ if isequal(Linked,0) %0 indicates Drugs and Media are combinatorial
DM.media(medCnt) = {raw(excLnNum,4)};
excLnNum=excLnNum+1;
end
else %else if not PC (Then linux or other)
else
excLnNum=1;
while (~isequal(DMcell{excLnNum+1,2},'###'))
drgCnt=drgCnt+1;
@@ -206,7 +315,5 @@ if isequal(Linked,0) %0 indicates Drugs and Media are combinatorial
msg=strcat('NumberOfDrugs = ',num2str(drgCnt), ' NumberOfMedias = ',num2str(medCnt) )
end
save (fullfile(MPdir,'MPDMmat'), 'fields','MP','DM','Linked');
cd(w)
msgbox(['Drug-Media-MasterPlate Annotation File Generation Complete'])
save(mpdmFile, 'fields','MP','DM','Linked');
msgbox([strcat('Drug-Media-MasterPlate Annotation File', mpdmFile,'Generation Complete')])