Clean up templates

workflow/templates/qhtcp/Code/GTAtemplate.R

@@ -1,27 +1,27 @@
 #GTA (GoTermAveraging) Starting (Working Directory is /Code) All paths relative to /Code
 #Your output  may not be reproducible as org.Sc.sgd.db is uploaded from Bioconductor R library and changes
 #Loops thru the number of experiments involved in study. JWR
-         Wstudy= getwd()
+Wstudy= getwd()
-         if (file.exists('../Exp1/ZScores/ZScores_Interaction.csv')){
+if (file.exists('../Exp1/ZScores/ZScores_Interaction.csv')){
-           inputFile <- '../Exp1/ZScores/ZScores_Interaction.csv'
+  inputFile <- '../Exp1/ZScores/ZScores_Interaction.csv'
-           expName= "Exp1"
+  expName= "Exp1"
-           dir.create("../GTAresults/Exp1")
+  dir.create("../GTAresults/Exp1")
-         }
+}
-         if (file.exists('../Exp2/ZScores/ZScores_Interaction.csv')){
+if (file.exists('../Exp2/ZScores/ZScores_Interaction.csv')){
-           inputFile[2] <- '../Exp2/ZScores/ZScores_Interaction.csv'
+  inputFile[2] <- '../Exp2/ZScores/ZScores_Interaction.csv'
-           expName[2]= "Exp2"
+  expName[2]= "Exp2"
-           dir.create("../GTAresults/Exp2")
+  dir.create("../GTAresults/Exp2")
-         }
+}
-         if (file.exists('../Exp3/ZScores/ZScores_Interaction.csv')){
+if (file.exists('../Exp3/ZScores/ZScores_Interaction.csv')){
-           inputFile[3] <- '../Exp3/ZScores/ZScores_Interaction.csv'
+  inputFile[3] <- '../Exp3/ZScores/ZScores_Interaction.csv'
-           expName[3]= "Exp3"
+  expName[3]= "Exp3"
-           dir.create("../GTAresults/Exp3")
+  dir.create("../GTAresults/Exp3")
-         }
+}
-         if (file.exists('../Exp4/ZScores/ZScores_Interaction.csv')){
+if (file.exists('../Exp4/ZScores/ZScores_Interaction.csv')){
-           inputFile[4] <- '../Exp4/ZScores/ZScores_Interaction.csv'
+  inputFile[4] <- '../Exp4/ZScores/ZScores_Interaction.csv'
-           expName[4]= "Exp4"
+  expName[4]= "Exp4"
-           dir.create("../GTAresults/Exp4")
+  dir.create("../GTAresults/Exp4")
-         }
+}
          
 outputPathGTA= "../GTAresults"
         #dir.create(outPathGTA)

workflow/templates/qhtcp/Code/StudyInfo.csv

@@ -2,4 +2,3 @@ ExpNumb,ExpLabel,BackgroundSD,ZscoreJoinSD,AnalysisBy
 1,ExpName1,NA,NA,UserInitials
 2,ExpName2,NA,NA,UserInitials
 3,ExpName3,NA,NA,UserInitials
-4,ExpName4,NA,NA,UserInitials

workflow/templates/qhtcp/Documentation/.~lock.QHTCP Analysis SystemRev2c.docx#

@@ -1 +0,0 @@
-,jwrodger,hartmanlab.genetics.uab.edu,24.05.2023 07:56,file:///home/jwrodger/.config/libreoffice/4;

workflow/templates/qhtcp/Exp2/ExpFrontend.m

@@ -1,214 +0,0 @@
-%Frontend240417.m
-%augmented ExpFrontend to provide a quick text archive and a robust
-%database ammenable archive
-%FrontEnd utility to copy source result sheet into Exp_ folders of
-%StudiesQHTCP/StudyName/Exp1(2,3,4). This allow the automation of path
-%capture to the StudiesDataArchieve.txt study log.
-%Select, copy and Capture Study Exp_ details to study log
-
-%Exp meta data collection 
-W=pwd;
-%Load results file meta data  into workspace
-try 
-ExpLabel= strcat('Exp',W(end))
-questdlg('\fontsize{20} Select the !!Results File','File Selection','OK', struct('Default','OK','Interpreter','tex'));
-[resFile,resPath]= uigetfile('*.txt')
-copyfile((fullfile(resPath,resFile)),fullfile(W))
-resDate= char(regexp(resFile, '(\d\d\_\d\d\d\d)|( \d\d\_\d\d\d\d|\d\d\d\d\d\d)','match'))
-cd ..
-Wstudy= pwd
-studyDate= datetime('now');
-S.sDate(1) = {studyDate};
-if ispc
-    lastSep=max(strfind(Wstudy,'\'))
-    studyName= Wstudy((lastSep+1):end)
-else
-    lastSep=max(strfind(Wstudy,'/'))
-    studyName= Wstudy((lastSep+1):end)
-end
-
-S.sDate(1)= {studyDate};
-S.sName(1)= {studyName}
-S.sPath(1)= {Wstudy}
-S.ELabel(1)= {ExpLabel}
-S.EresDate(1)= {resDate}
-S.EresFile(1)= {resFile}
-S.EresPath(1)= {resPath}
-   
-cd ..
-
-fid = fopen('StudiesDataArchive.txt','a');  
-fprintf(fid,'StudyDate\tStudyName\tStudyPath\tExpNum\tExpDate\tExpPath\tResultFile\n');
-fprintf(fid, '%s\t %s\t %s\t %s\t %s\t %s\t %s \n',S.sDate{1},S.sName{1},S.sPath{1},S.ELabel{1},S.EresDate{1},S.EresPath{1},S.EresFile{1});
-fclose(fid);
-fclose('all');
-
-catch
-    cd(W)
-    disp('Error: Unable to Execute ExpFrontend.m')
-end
-
-cd(W)
-pwd
-
-
-
-%*************************************************************************************
-%*************************************************************************************
-%#####################################################################################
-%Improved storage ammenable for database use
-%FrontEnd utility to copy source result sheet into Exp_ folders of
-%StudiesQHTCP/StudyName/Exp1(2,3,4). This allow the automation of path
-%capture to the StudiesDataArchieve.txt study log.
-%Select, copy and Capture Study Exp_ details to study log
-studyDateNow= studyDate  %preserve the 'Now' date 
-nowNumFNm= strcat((int2str(now)),'.mat') % from previous section incase the /StudyName doesn't have a standard date 
-%capture the /StudiesQHTCP directory for storing log data
-cd ../..
-logPath= pwd  %is /.../Exp_
-cd(W)
-%Try to load an existing data set from previous Frontend calls
-try  %end ~ln121
-  load(fullfile(logPath,'.studyLog.mat')) %load(fullfile('../../','studyLog.mat'))
-catch  %If no studyLog.mat found [Initial First Entry]
-    ExpLabel= strcat('Exp',W(end))
-    resDate= char(regexp(resFile, '(\d\d\_\d\d\d\d)|( \d\d\_\d\d\d\d|\d\d\d\d\d\d)','match'))
-    cd .. %move up to current study folder from ../Exp_ folder; 
-    %Study meta data collection
-    Wstudy= pwd %Capture the specific current Study directory
-    try %try to extract study date from folder name
-     studyDate= char(regexp(Wstudy, '(\d\d\_\d\d\d\d)|( \d\d\_\d\d\d\d|\d\d\d\d\d\d)| \d\d\d\d\d\d)','match'))
-     S.sDate(1)= {studyDate};
-    catch %if unsuccessful, accept the current date and convert to a 6 char string
-     studyDate= yyyymmdd(studyDateNow);
-     studyDate= (int2str(studyDate))
-     studyDate= studyDate(3:8)
-    end
-   %Capture StudyName
-   if ispc
-    lastSep=max(strfind(Wstudy,'\'))
-    studyName= Wstudy((lastSep+1):end)
-   else
-    lastSep=max(strfind(Wstudy,'/'))
-    studyName= Wstudy((lastSep+1):end)
-    
-   end
-  %Put current First data entry into Structure of Save to StudyLog.mat file
-   S.sDate(1)= {studyDate};
-   S.sName(1)= {studyName}
-   S.sPath(1)= {Wstudy}
-   S.ELabel(1)= {ExpLabel}
-   S.EresDate(1)= {resDate}
-   S.EresFile(1)= {resFile}
-   S.EresPath(1)= {resPath}
-   
- cd(W)
-
-logFiletxt= fullfile(logPath,'StudiesDataArchive4DB.txt') %relative .txt path 
-%Initialize the StudiesDataArchive.txt file with the First row of meta data
-
-%Print to a .txt spreadsheet the first set of data in the logFiletxt file
-fid = fopen(logFiletxt,'w');
-fprintf(fid,'StudyDate\tStudyName\tStudyPath\tExpNum\tExpDate\tExpPath\tResultFile\n');
-fprintf(fid, '%s\t %s\t %s\t %s\t %s\t %s\t %s \n',studyDate,studyName,Wstudy,ExpLabel,resDate,resPath,resFile);
-fclose(fid);
-%Save the first entry meta data into a permanent .mat files for future recall
-save(fullfile(logPath,'studyLog4DB.mat'), 'S')
-save(fullfile(logPath,'.studyLog.mat'), 'S')
-save(fullfile(logPath,'.nowNumFNm.mat'), 'S')
-
-
-
-end  %end for try  for the First entry only
-%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-%++++++++END of FIRST ENTRY startup section++++++++++++++++++++++++++++++++
-%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-
-
-
-%Begin routine for all Entries After the Initial data entry**************** 
-ExpLabel= strcat('Exp',W(end))
-resDate= char(regexp(resFile, '(\d\d\_\d\d\d\d)|( \d\d\_\d\d\d\d|\d\d\d\d\d\d)','match')) %Capture date from !!Results file
-
-cd .. %Move to the current study folder
-
-%Capture study meta dat
-Wstudy= pwd % Capture the path to the current study
-
-  %Attempt to extract study date from folder name and convert to a
-  %searchable numeric date
-   studyDate= char(regexp(Wstudy, '(\d\d\_\d\d\d\d)|( \d\d\_\d\d\d\d|\d\d\d\d\d\d)| \d\d\d\d\d\d)','match'))
-      if ~isempty(studyDate)  %If no date in folder name use current date and convert to 6char string
-       S.sDate(1)= {studyDate};
-       if isequal((str2num(studyDate(3))),'_') %Remove '_' so that date is a number for easy DB search
-           studyDate= strcat(studyDate(1:2),studyDate(4:6))
-       end
-      else
-       studyDate= yyyymmdd(studyDateNow);
-       studyDate= (int2str(studyDate)) 
-       studyDate= studyDate(3:8) 
-     end
-    
-if ispc
-    lastSep=max(strfind(Wstudy,'\'))
-    studyName= Wstudy((lastSep+1):end)
-else
-    lastSep=max(strfind(Wstudy,'/'))
-    studyName= Wstudy((lastSep+1):end)
-end
-
-%Put meta data into a structure for storage (studyLog.mat) and future
-%compare operations
-lastRow= length(S.sPath)
-
-%Compare these just obtained paths with those stored in the studyLog.mat
-%file and add a new row if the study or results sheet meta data is new or different
-cd ..  %Move the the /QHTPCstudies folder
-logtxt= 'StudiesDataArchive4DB.txt'
-logFiletxt= fullfile(logPath,logtxt) %
-try
-  matched=0;
- for n= 1:(lastRow)
-    if strcmp(Wstudy,S.sPath(n)) && strcmp(resPath, S.EresPath(n)) && strcmp(ExpLabel, S.ELabel(n))
-        matched= 1;
-        break
-    end
- end
-      
-    
-%Update the StudiesDataArchive.txt file with a new row of meta data
-if matched== 0 %if no match for this entry then add a line to the text archive file
-     fid = fopen(logFiletxt,'w');  
-      S.sDate(lastRow+1)= {studyDate};
-      S.sName(lastRow+1)= {studyName};
-      S.sPath(lastRow+1)= {Wstudy};
-      S.ELabel(lastRow+1)= {ExpLabel};
-      S.EresDate(lastRow+1)= {resDate};
-      S.EresFile(lastRow+1)= {resFile};
-      S.EresPath(lastRow+1)= {resPath};
-  for n= 1:(lastRow +1)
-   %Print to a .txt spreadsheet and Save update to .mat files
-    if n==1
-     fprintf(fid,'StudyDate\tStudyName\tStudyPath\tExpNum\tExpDate\tExpPath\tResultFile\n');
-    end
-    fprintf(fid, '%s\t %s\t %s\t %s\t %s\t %s\t %s \n',S.sDate{n},S.sName{n},S.sPath{n},S.ELabel{n},S.EresDate{n},S.EresPath{n},S.EresFile{n});
-  end
-
-  fclose(fid); %close DBase amenable study log file after data update
- 
- save((fullfile(logPath,'studyLog4DB.mat')), 'S') % path for  studyLog.mat
- save((fullfile(logPath,'.studyLog.mat')), 'S')  %path backup studyLogBU.mat
- save((fullfile(logPath,strcat('.',nowNumFNm))), 'S') 
-end 
-fclose('all');
-
-catch
-    cd(W) %Return to the location of the frontend.m code (/studyName/Exp_)
-    fclose('all');
-    clear S %clear data structure variable 'S.'
-end
-
-cd(W) %Return to the location of the frontend.m code (/studyName/Exp_)
-clear all %clear workspace variables
-
-

workflow/templates/qhtcp/Exp3/ExpFrontend.m

@@ -1,53 +0,0 @@
-%FrontEnd utility to copy source result sheet into Exp_ folders of
-%StudiesQHTCP/StudyName/Exp1(2,3,4). This allow the automation of path
-%capture to the StudiesDataArchieve.txt study log.
-%Select, copy and Capture Study Exp_ details to study log
-
-%Exp meta data collection 
-W=pwd;
-%Load matlab stored data file into workspace
-try 
-ExpLabel= strcat('Exp',W(end))
-questdlg('\fontsize{20} Select the !!Results File','File Selection','OK', struct('Default','OK','Interpreter','tex'));
-[resFile,resPath]= uigetfile('*.txt')
-copyfile((fullfile(resPath,resFile)),fullfile(W))
-resDate= char(regexp(resFile, '(\d\d\_\d\d\d\d)|( \d\d\_\d\d\d\d|\d\d\d\d\d\d)','match'))
-cd ..
-Wstudy= pwd
-studyDate= datetime("today");
-S.sDate(1) = {studyDate};
-if ispc
-    lastSep=max(strfind(Wstudy,'\'))
-    studyName= Wstudy((lastSep+1):end)
-else
-    lastSep=max(strfind(Wstudy,'/'))
-    studyName= Wstudy((lastSep+1):end)
-end
-
-S.sDate(1)= {studyDate};
-S.sName(1)= {studyName}
-S.sPath(1)= {Wstudy}
-S.ELabel(1)= {ExpLabel}
-S.EresDate(1)= {resDate}
-S.EresFile(1)= {resFile}
-S.EresPath(1)= {resPath}
-   
-cd ..
-
-fid = fopen('StudiesDataArchive.txt','a');  
-fprintf(fid,'StudyDate\tStudyName\tStudyPath\tExpNum\tExpDate\tExpPath\tResultFile\n');
-fprintf(fid, '%s\t %s\t %s\t %s\t %s\t %s\t %s \n',S.sDate{1},S.sName{1},S.sPath{1},S.ELabel{1},S.EresDate{1},S.EresPath{1},S.EresFile{1});
-fclose(fid);
-%save((fullfile(pwd,'studyLog.mat')), 'S')  
-fclose('all');
-
-catch
-    cd(W)
-    disp('Error: Unable to Execute ExpFrontend.m')
-end
-
-
-
-
-
-

workflow/templates/qhtcp/Exp4/ExpFrontend.m

@@ -1,53 +0,0 @@
-%FrontEnd utility to copy source result sheet into Exp_ folders of
-%StudiesQHTCP/StudyName/Exp1(2,3,4). This allow the automation of path
-%capture to the StudiesDataArchieve.txt study log.
-%Select, copy and Capture Study Exp_ details to study log
-
-%Exp meta data collection 
-W=pwd;
-%Load matlab stored data file into workspace
-try 
-ExpLabel= strcat('Exp',W(end))
-questdlg('\fontsize{20} Select the !!Results File','File Selection','OK', struct('Default','OK','Interpreter','tex'));
-[resFile,resPath]= uigetfile('*.txt')
-copyfile((fullfile(resPath,resFile)),fullfile(W))
-resDate= char(regexp(resFile, '(\d\d\_\d\d\d\d)|( \d\d\_\d\d\d\d|\d\d\d\d\d\d)','match'))
-cd ..
-Wstudy= pwd
-studyDate= datetime("today");
-S.sDate(1) = {studyDate};
-if ispc
-    lastSep=max(strfind(Wstudy,'\'))
-    studyName= Wstudy((lastSep+1):end)
-else
-    lastSep=max(strfind(Wstudy,'/'))
-    studyName= Wstudy((lastSep+1):end)
-end
-
-S.sDate(1)= {studyDate};
-S.sName(1)= {studyName}
-S.sPath(1)= {Wstudy}
-S.ELabel(1)= {ExpLabel}
-S.EresDate(1)= {resDate}
-S.EresFile(1)= {resFile}
-S.EresPath(1)= {resPath}
-   
-cd ..
-
-fid = fopen('StudiesDataArchive.txt','a');  
-fprintf(fid,'StudyDate\tStudyName\tStudyPath\tExpNum\tExpDate\tExpPath\tResultFile\n');
-fprintf(fid, '%s\t %s\t %s\t %s\t %s\t %s\t %s \n',S.sDate{1},S.sName{1},S.sPath{1},S.ELabel{1},S.EresDate{1},S.EresPath{1},S.EresFile{1});
-fclose(fid);
-%save((fullfile(pwd,'studyLog.mat')), 'S')  
-fclose('all');
-
-catch
-    cd(W)
-    disp('Error: Unable to Execute ExpFrontend.m')
-end
-
-
-
-
-
-