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Remove old PROJECT vars

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Bryan Roessler
2024-08-04 17:10:01 -04:00
parent 37589ce8e3
commit e8b8905c8b
2 changed files with 36 additions and 24 deletions
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workflow/README.md
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@@ -37,7 +37,7 @@ Insert a general description of Q-HTCP and the Q-HTCP process here.
## Notes
### TO-DO
### TODO
* Variable scoping is horrible right now
* I wrote this sequentially and tried to keep track the best I could
@@ -70,6 +70,28 @@ Insert a general description of Q-HTCP and the Q-HTCP process here.
* The QHTCPImageFolders and 'MasterPlateFiles' folder are the inputs for image analysis with EASY software.
* 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.
      **apps/easy/**
* This directory contains the GUI-enabled MATLAB software to accomplish image analysis and growth curve fitting.
* 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).
* 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.
* 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).
* The /EASY directory is simply where the latest EASY version resides (additional versions in development or legacy versions may also be stored there).
* The raw data inputs and result outputs for EASY are kept in the 'ExpJobs' directory.
* 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.
      **apps/ezview/**
* This directory contains the GUI-enabled MATLAB software to conveniently and efficiently mine the raw cell array image data for a Q-HTCP experiment.
* 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.
* The /EZview provides a place for storing the the latest EZview version (as well as other EZview versions).
* The /EZview provides a GUI for examining the EASY results as provided in the …/matResults/… .mat file.
      **Master Plates**
* 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.
* 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.
### parse_input
`--project`, `--module`, `--nomodule`, and `--submodule` can be passed multiple times or with a comma-separated string
@@ -200,6 +222,7 @@ TODO
* Don't create output in the scans folder, put it in an output directory
* The !!Results output files need standardized naming
* The input MasterPlate and DrugMedia sheets need to be converted to something standard like csv/tsv
* This would allow them to be created programmatically as well
NOTES
@@ -545,7 +568,7 @@ TODO
Files
* gene_association.sgd: https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd
* [gene_association.sgd](https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd)
* go_terms.tab
Output
@@ -557,7 +580,7 @@ Output
* **$1** (string): Exp# name
* **$2** (string): ZScores_Interaction.csv file
* **$3** (string): go_terms.tab file
* **$4** (string): gene_association.sgd
* **$4** (string): [gene_association.sgd](https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd)
* **$5** (string): output directory
### r_gta_pairwiselk
@@ -632,7 +655,7 @@ Run the R interactions analysis (Z_InteractionTemplate.R)
TODO
* don't want to rename Z_InteractionTemplate.R because that will break logic, just edit in place instead
* Don't want to rename Z_InteractionTemplate.R because that will break logic, just edit in place instead
NOTES
@@ -776,12 +799,6 @@ TODO
* Expanded into a file that stores all project/study settings (database)
* I had to had a new line to the end of StudyInfo.csv, may break things?
Example:
ExpNumb,ExpLabel,BackgroundSD,ZscoreJoinSD,AnalysisBy
1,ExpName1,NA,NA,UserInitials
2,ExpName2,NA,NA,UserInitials
3,ExpName3,NA,NA,UserInitials
#### Arguments
* **$1** (string): File to read