Remove old PROJECT vars
This commit is contained in:
@@ -37,7 +37,7 @@ Insert a general description of Q-HTCP and the Q-HTCP process here.
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## Notes
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### TO-DO
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### TODO
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* Variable scoping is horrible right now
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* I wrote this sequentially and tried to keep track the best I could
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@@ -70,6 +70,28 @@ Insert a general description of Q-HTCP and the Q-HTCP process here.
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* The QHTCPImageFolders and 'MasterPlateFiles' folder are the inputs for image analysis with EASY software.
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* As further described below, EASY will automatically generate a 'Results' directory (within the ExpJobs/'ExperimentJob' folder) with a name that consists of a system-generated timestamp and an optional short description provided by the user (Fig.2). The 'Results' directory is created and entered, using the "File >> New Experiment" dropdown in EASY. Multiple 'Results' files may be created (and uniquely named) within an 'ExperimentJob' folder.
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**apps/easy/**
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* This directory contains the GUI-enabled MATLAB software to accomplish image analysis and growth curve fitting.
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* EASY analyzes Q-HTCP image data within an 'ExperimentJob'' folder (described above; each cell array has its own folder containing its entire time series of images).
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* EASY analysis produces image quantification data and growth curve fitting results for each cell array; these results are subsequently assembled into a single file and labeled, using information contained in the 'MasterPlate_' and 'DrugMedia_' files in the 'MasterPlateFiles' subdirectory.
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* The final files (named '!!ResultsStd_.txt' or '!!ResultsELr_.txt') are produced in a subdirectory that EASY creates within the 'ExpJob#' folder, named '/ResultsTimeStampDesc/PrintResults' (Fig. 2).
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* The /EASY directory is simply where the latest EASY version resides (additional versions in development or legacy versions may also be stored there).
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* The raw data inputs and result outputs for EASY are kept in the 'ExpJobs' directory.
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* EASY also outputs a '.mat' file that is stored in the 'matResults' folder and is named with the TimeStamp and user-provided name appended to the 'Results' folder name when 'New Experiment' is executed from the 'File' Dropdown menu in the EASY console.
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**apps/ezview/**
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* This directory contains the GUI-enabled MATLAB software to conveniently and efficiently mine the raw cell array image data for a Q-HTCP experiment.
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* It takes the Results.m file (created by EASY software) as an input and permits the user to navigate through the raw image data and growth curve results for the experiment.
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* The /EZview provides a place for storing the the latest EZview version (as well as other EZview versions).
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* The /EZview provides a GUI for examining the EASY results as provided in the …/matResults/… .mat file.
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**Master Plates**
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* This optional folder is a convenient place to store copies of the 'MasterPlate_' and a 'DrugMedia_' file templates, along with previously used files that may have been modified and could be reused or further modified to enable future analyses.
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* These two file types are required in the 'MasterPlateFiles' folder, which catalogs experimental information specific to individual Jobs in the ExpJobs folder, as described further below.
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### parse_input
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`--project`, `--module`, `--nomodule`, and `--submodule` can be passed multiple times or with a comma-separated string
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@@ -200,6 +222,7 @@ TODO
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* Don't create output in the scans folder, put it in an output directory
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* The !!Results output files need standardized naming
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* The input MasterPlate and DrugMedia sheets need to be converted to something standard like csv/tsv
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* This would allow them to be created programmatically as well
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NOTES
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@@ -545,7 +568,7 @@ TODO
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Files
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* gene_association.sgd: https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd
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* [gene_association.sgd](https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd)
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* go_terms.tab
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Output
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@@ -557,7 +580,7 @@ Output
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* **$1** (string): Exp# name
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* **$2** (string): ZScores_Interaction.csv file
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* **$3** (string): go_terms.tab file
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* **$4** (string): gene_association.sgd
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* **$4** (string): [gene_association.sgd](https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd)
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* **$5** (string): output directory
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### r_gta_pairwiselk
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@@ -632,7 +655,7 @@ Run the R interactions analysis (Z_InteractionTemplate.R)
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TODO
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* don't want to rename Z_InteractionTemplate.R because that will break logic, just edit in place instead
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* Don't want to rename Z_InteractionTemplate.R because that will break logic, just edit in place instead
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NOTES
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@@ -776,12 +799,6 @@ TODO
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* Expanded into a file that stores all project/study settings (database)
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* I had to had a new line to the end of StudyInfo.csv, may break things?
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Example:
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ExpNumb,ExpLabel,BackgroundSD,ZscoreJoinSD,AnalysisBy
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1,ExpName1,NA,NA,UserInitials
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2,ExpName2,NA,NA,UserInitials
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3,ExpName3,NA,NA,UserInitials
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#### Arguments
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* **$1** (string): File to read
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@@ -78,7 +78,7 @@ print_help() {
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# @section Notes
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# @description
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#
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# ### TO-DO
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# ### TODO
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#
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# * Variable scoping is horrible right now
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# * I wrote this sequentially and tried to keep track the best I could
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@@ -110,7 +110,7 @@ print_help() {
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# * Together they encapsulate and define the experimental design.
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# * The QHTCPImageFolders and 'MasterPlateFiles' folder are the inputs for image analysis with EASY software.
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# * As further described below, EASY will automatically generate a 'Results' directory (within the ExpJobs/'ExperimentJob' folder) with a name that consists of a system-generated timestamp and an optional short description provided by the user (Fig.2). The 'Results' directory is created and entered, using the "File >> New Experiment" dropdown in EASY. Multiple 'Results' files may be created (and uniquely named) within an 'ExperimentJob' folder.
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#
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# **apps/easy/**
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#
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# * This directory contains the GUI-enabled MATLAB software to accomplish image analysis and growth curve fitting.
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@@ -120,7 +120,7 @@ print_help() {
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# * The /EASY directory is simply where the latest EASY version resides (additional versions in development or legacy versions may also be stored there).
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# * The raw data inputs and result outputs for EASY are kept in the 'ExpJobs' directory.
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# * EASY also outputs a '.mat' file that is stored in the 'matResults' folder and is named with the TimeStamp and user-provided name appended to the 'Results' folder name when 'New Experiment' is executed from the 'File' Dropdown menu in the EASY console.
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#
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# **apps/ezview/**
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#
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# * This directory contains the GUI-enabled MATLAB software to conveniently and efficiently mine the raw cell array image data for a Q-HTCP experiment.
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@@ -134,8 +134,6 @@ print_help() {
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# * These two file types are required in the 'MasterPlateFiles' folder, which catalogs experimental information specific to individual Jobs in the ExpJobs folder, as described further below.
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#
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#
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# Some example decorators for markdown:
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#
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#
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# @description
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# `--project`, `--module`, `--nomodule`, and `--submodule` can be passed multiple times or with a comma-separated string
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@@ -366,7 +364,6 @@ interactive_header() {
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echo "Example: SCANS_DIR=/path/to/scans OUT_DIR=/path/to/out ./qhtcp-workflow $*"
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echo ""
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# Ask to make our custom R library the default
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if [[ -z $R_LIBS_USER || $R_LIBS_USER != "$HOME/R/$SCRIPT_NAME" ]]; then
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echo "This script uses a local R library at $HOME/R/$SCRIPT_NAME"
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@@ -1138,8 +1135,8 @@ easy() {
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done
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# Copy Templates
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declare -gx DRUG_MEDIA_FILE="$EASY_RESULTS_DIR/DrugMedia_$PROJECT.xls"
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declare -gx MASTER_PLATE_FILE="$EASY_RESULTS_DIR/MasterPlate_$PROJECT.xls"
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declare -gx DRUG_MEDIA_FILE="$EASY_RESULTS_DIR/DrugMedia_$PROJECT_NAME.xls"
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declare -gx MASTER_PLATE_FILE="$EASY_RESULTS_DIR/MasterPlate_$PROJECT_NAME.xls"
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rsync -a "$EASY_DIR"/{figs,PTmats} "$EASY_RESULTS_DIR"
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# Ask the user to launch EASYconsole.m in MATLAB
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@@ -1345,7 +1342,7 @@ qhtcp() {
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for s in "${STUDIES_NUMS[@]}"; do
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# Trying to match old ExpFrontend formatting
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printf "%s\t" \
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"${DATE//_/}" "$PROJECT" "$QHTCP_PROJECT_DIR" "Exp$s" \
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"${DATE//_/}" "$PROJECT_NAME" "$QHTCP_PROJECT_DIR" "Exp$s" \
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"$PROJECT_DATE" "$PROJECT_SCANS_DIR" "$EASY_RESULTS_DIR" "${f##*/}" \
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>> "$STUDIES_ARCHIVE_FILE"
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done
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@@ -1955,16 +1952,14 @@ submodule get_studies
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# * Expanded into a file that stores all project/study settings (database)
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# * I had to had a new line to the end of StudyInfo.csv, may break things?
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#
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# Example:
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# ExpNumb,ExpLabel,BackgroundSD,ZscoreJoinSD,AnalysisBy
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# 1,ExpName1,NA,NA,UserInitials
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# 2,ExpName2,NA,NA,UserInitials
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# 3,ExpName3,NA,NA,UserInitials
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#
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#
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# @exitcode 0 If one or more studies found
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# @exitcode 1 If no studies found
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# @set STUDIES_NUMS array Contains Exp numbers
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# @set NUM_STUDIES int Number of existing studies
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# @arg $1 string File to read
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#
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get_studies() {
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debug "Running: ${FUNCNAME[0]}"
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declare -ga STUDIES_NUMS=()
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