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Finish PairwiseLK module

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This commit is contained in:
Bryan Roessler
2024-07-24 21:11:25 -04:00
parent 7b8ce3e7fd
commit ef449c66ff
6 changed files with 594 additions and 481 deletions
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workflow/script-run-workflow
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@@ -5,8 +5,7 @@
# Allow indirect functions # Allow indirect functions
# shellcheck disable=SC2317 # shellcheck disable=SC2317
# #
# shdoc info # @name Hartman Lab Self-Documenting Workflow
# @name HartmanLabWorkflow
# @brief One script to rule them all (see: xkcd #927) # @brief One script to rule them all (see: xkcd #927)
# @description A flexible yet opinionated analysis framework for the Hartman Lab # @description A flexible yet opinionated analysis framework for the Hartman Lab
# There should be at least 4 subdirectories to organize Q-HTCP data and analysis. The parent directory is simply called 'Q-HTCP' and the 4 are subdirectories described below (Fig. 1): # There should be at least 4 subdirectories to organize Q-HTCP data and analysis. The parent directory is simply called 'Q-HTCP' and the 4 are subdirectories described below (Fig. 1):
@@ -27,7 +26,6 @@
DEBUG=1 # Turn debugging ON by default during development DEBUG=1 # Turn debugging ON by default during development
shopt -s extglob shopt -s extglob
# @section Libraries # @section Libraries
# @description Change these variables to use different libraries # @description Change these variables to use different libraries
JAVA="${JAVA:-java}" JAVA="${JAVA:-java}"
@@ -59,7 +57,7 @@ print_help() {
--exclude, -x MODULE --exclude, -x MODULE
See MODULES section below for list of modules to exclude See MODULES section below for list of modules to exclude
--markdown, -m --markdown, -m
Generate the shdoc markdown file for this program Generate the shdoc markdown README.md file for this program
--yes, -y, --auto --yes, -y, --auto
Always answer yes to questions (non-interactive mode) Always answer yes to questions (non-interactive mode)
--debug, -d --debug, -d
@@ -135,7 +133,7 @@ parse_input() {
fi fi
;; ;;
--markdown|-m) --markdown|-m)
documentation documentation; exit 0 # TODO disable the exit after development
;; ;;
--yes|-y|--auto) --yes|-y|--auto)
declare -g YES=1 declare -g YES=1
@@ -542,303 +540,6 @@ module qhtcp
# As stated above, it is advantageous to think about the comparisons one wishes to make so as to order the experiments in a rational way as it relates to the presentation of plots. That is, which results from sheets and selected 'interaction … .R', user modified script, is used in /Exp1, Exp2, Exp3 and Exp4 as explained in the following section. # As stated above, it is advantageous to think about the comparisons one wishes to make so as to order the experiments in a rational way as it relates to the presentation of plots. That is, which results from sheets and selected 'interaction … .R', user modified script, is used in /Exp1, Exp2, Exp3 and Exp4 as explained in the following section.
# TODO MUST CLEAN UP QHTCP TEMPLATE DIRECTORY # TODO MUST CLEAN UP QHTCP TEMPLATE DIRECTORY
# #
# Template:
# templates/qhtcp
# * [A_QHTCP Study Design and Notes](templates/qhtcp/A_QHTCP Study Design and Notes)
# * [A_Suggestions for system improvements.odt](templates/qhtcp/A_QHTCP Study Design and Notes/A_Suggestions for system improvements.odt)
# * [QHTCP Study Design and Notes.odt](templates/qhtcp/A_QHTCP Study Design and Notes/QHTCP Study Design and Notes.odt)
# * [Code](templates/qhtcp/Code)
# * [22_0602_Remy_DAmPsList.txt](templates/qhtcp/Code/22_0602_Remy_DAmPsList.txt)
# * [All_SGD_GOTerms.csv](templates/qhtcp/Code/All_SGD_GOTerms.csv)
# * [All_SGD_GOTerms_for_QHTCPtk.csv](templates/qhtcp/Code/All_SGD_GOTerms_for_QHTCPtk.csv)
# * [devStuff](templates/qhtcp/Code/devStuff)
# * [InteractTemplateB4fixes.R](templates/qhtcp/Code/devStuff/InteractTemplateB4fixes.R)
# * [InteractTemplateB4Prompt4SDinput.R](templates/qhtcp/Code/devStuff/InteractTemplateB4Prompt4SDinput.R)
# * [gene_association.sgd](templates/qhtcp/Code/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/Code/gene_ontology_edit.obo)
# * [go_terms.tab](templates/qhtcp/Code/go_terms.tab)
# * [GTAtemplate.R](templates/qhtcp/Code/GTAtemplate.R)
# * [ORF_List_DAmPs_Only.txt](templates/qhtcp/Code/ORF_List_DAmPs_Only.txt)
# * [ORF_List_Without_DAmPs.txt](templates/qhtcp/Code/ORF_List_Without_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/Code/ORFs_w_DAmP_list.txt)
# * [PairwiseLK.R](templates/qhtcp/Code/PairwiseLK.R)
# * [Parameters.csv](templates/qhtcp/Code/Parameters.csv)
# * [RenameFiles2.sh](templates/qhtcp/Code/RenameFiles2.sh)
# * [ScriptTemplates](templates/qhtcp/Code/ScriptTemplates)
# * [BU_Legacy](templates/qhtcp/Code/ScriptTemplates/BU_Legacy)
# * [InteractTemplate.R](templates/qhtcp/Code/ScriptTemplates/BU_Legacy/InteractTemplate.R)
# * [Concatenate_GTF_resultsB4REMcMaster2.py](templates/qhtcp/Code/ScriptTemplates/Concatenate_GTF_resultsB4REMcMaster2.py)
# * [Concatenate_GTF_results.py](templates/qhtcp/Code/ScriptTemplates/Concatenate_GTF_results.py)
# * [GTAtemplate.R](templates/qhtcp/Code/ScriptTemplates/GTAtemplate.R)
# * [InteractionTemplate230119.R](templates/qhtcp/Code/ScriptTemplates/InteractionTemplate230119.R)
# * [JoinInteractExps3dev.R](templates/qhtcp/Code/ScriptTemplates/JoinInteractExps3dev.R)
# * [JoinInteractExps.R](templates/qhtcp/Code/ScriptTemplates/JoinInteractExps.R)
# * [PairwiseK_lbl.R](templates/qhtcp/Code/ScriptTemplates/PairwiseK_lbl.R)
# * [PairwiseLK.R](templates/qhtcp/Code/ScriptTemplates/PairwiseLK.R)
# * [PairwiseL_lbl.R](templates/qhtcp/Code/ScriptTemplates/PairwiseL_lbl.R)
# * [Remy_yor_dF_correlation_study.R](templates/qhtcp/Code/ScriptTemplates/Remy_yor_dF_correlation_study.R)
# * [TSHeatmaps5dev2.R](templates/qhtcp/Code/ScriptTemplates/TSHeatmaps5dev2.R)
# * [SGD_features.tab](templates/qhtcp/Code/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/Code/SGD_features.tab.txt)
# * [SSscripts](templates/qhtcp/Code/SSscripts)
# * [18_0205_heatmaps_zscores_2SD_color_NARem_Z_lm.R](templates/qhtcp/Code/SSscripts/18_0205_heatmaps_zscores_2SD_color_NARem_Z_lm.R)
# * [22_0603_Remy_Exclude_DAmPs.R](templates/qhtcp/Code/SSscripts/22_0603_Remy_Exclude_DAmPs.R)
# * [cmd_Doxo_SumZScore_Z_lm_Interaction_drug_all_rm_onedrug_V4_yor1_with_Dox_validationedit.R](templates/qhtcp/Code/SSscripts/cmd_Doxo_SumZScore_Z_lm_Interaction_drug_all_rm_onedrug_V4_yor1_with_Dox_validationedit.R)
# * [cmd_ScoreAllGOTerms_From_Z_lm_V2.R](templates/qhtcp/Code/SSscripts/cmd_ScoreAllGOTerms_From_Z_lm_V2.R)
# * [Compare_GTF_Averages_BetweenScreens_lm_Kvals_v2.R](templates/qhtcp/Code/SSscripts/Compare_GTF_Averages_BetweenScreens_lm_Kvals_v2.R)
# * [Compare_GTF_Averages_BetweenScreens_lm_Lvals_v2.R](templates/qhtcp/Code/SSscripts/Compare_GTF_Averages_BetweenScreens_lm_Lvals_v2.R)
# * [Compare_GTF_Averages_BetweenScreens_lm_v2.R](templates/qhtcp/Code/SSscripts/Compare_GTF_Averages_BetweenScreens_lm_v2.R)
# * [GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_3terms_V2.R](templates/qhtcp/Code/SSscripts/GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_3terms_V2.R)
# * [GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_4terms_aging.R](templates/qhtcp/Code/SSscripts/GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_4terms_aging.R)
# * [GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_4terms_v2.R](templates/qhtcp/Code/SSscripts/GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_4terms_v2.R)
# * [GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_5terms_V2.R](templates/qhtcp/Code/SSscripts/GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_5terms_V2.R)
# * [GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_V2.R](templates/qhtcp/Code/SSscripts/GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_V2.R)
# * [ScoreAllGOTerms_From_Z_lm_V2.R](templates/qhtcp/Code/SSscripts/ScoreAllGOTerms_From_Z_lm_V2.R)
# * [StudyInfo.csv](templates/qhtcp/Code/StudyInfo.csv)
# * [TSHeatmaps5dev2.R](templates/qhtcp/Code/TSHeatmaps5dev2.R)
# * [Updating files](templates/qhtcp/Code/Updating files)
# * [23_0929](templates/qhtcp/Code/Updating files/23_0929)
# * [gene_association.sgd](templates/qhtcp/Code/Updating files/23_0929/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/Code/Updating files/23_0929/gene_ontology_edit.obo)
# * [go_terms.tab](templates/qhtcp/Code/Updating files/23_0929/go_terms.tab)
# * [ORFs_NO_DAmPs.txt](templates/qhtcp/Code/Updating files/23_0929/ORFs_NO_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/Code/Updating files/23_0929/ORFs_w_DAmP_list.txt)
# * [SGD_features.tab](templates/qhtcp/Code/Updating files/23_0929/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/Code/Updating files/23_0929/SGD_features.tab.txt)
# * [original_outdated](templates/qhtcp/Code/Updating files/original_outdated)
# * [gene_association.sgd](templates/qhtcp/Code/Updating files/original_outdated/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/Code/Updating files/original_outdated/gene_ontology_edit.obo)
# * [go_terms.tab](templates/qhtcp/Code/Updating files/original_outdated/go_terms.tab)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/Code/Updating files/original_outdated/ORFs_w_DAmP_list.txt)
# * [SGD_features.tab](templates/qhtcp/Code/Updating files/original_outdated/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/Code/Updating files/original_outdated/SGD_features.tab.txt)
# * [SGDFeatureUpdates](templates/qhtcp/Code/Updating files/SGDFeatureUpdates)
# * [23_0927_SGDFeatures for KO.DAmP_library.csv](templates/qhtcp/Code/Updating files/SGDFeatureUpdates/23_0927_SGDFeatures for KO.DAmP_library.csv)
# * [23_0927_SGDFeatures for KO.DAmP_library.tsv](templates/qhtcp/Code/Updating files/SGDFeatureUpdates/23_0927_SGDFeatures for KO.DAmP_library.tsv)
# * [copy of original files before updates](templates/qhtcp/Code/Updating files/SGDFeatureUpdates/copy of original files before updates)
# * [SGD_features.tab_updates.xlsx](templates/qhtcp/Code/Updating files/SGDFeatureUpdates/SGD_features.tab_updates.xlsx)
# * [SGD_features_UPDATES for 2 files.xlsx](templates/qhtcp/Code/Updating files/SGDFeatureUpdates/SGD_features_UPDATES for 2 files.xlsx)
# * [SGD readme files](templates/qhtcp/Code/Updating files/SGD readme files)
# * [gene_association.README](templates/qhtcp/Code/Updating files/SGD readme files/gene_association.README)
# * [go_terms.README](templates/qhtcp/Code/Updating files/SGD readme files/go_terms.README)
# * [_Updating_Notes_23_0329.txt](templates/qhtcp/Code/Updating files/_Updating_Notes_23_0329.txt)
# * [Updating Q-HTCP_SourceFiles.docx](templates/qhtcp/Code/Updating files/Updating Q-HTCP_SourceFiles.docx)
# * [Documentation](templates/qhtcp/Documentation)
# * [20_0329_SS_Q_HTCP_Analysis_Readme.docx](templates/qhtcp/Documentation/20_0329_SS_Q_HTCP_Analysis_Readme.docx)
# * [Jingyu_REMc_Instruction for clustering and heatmap plotting _updated2013Mar.docx](templates/qhtcp/Documentation/Jingyu_REMc_Instruction for clustering and heatmap plotting _updated2013Mar.docx)
# * [ExpTemplate](templates/qhtcp/ExpTemplate)
# * [backups](templates/qhtcp/ExpTemplate/backups)
# * [InteractTemplateB4Prompt4SDinput.R](templates/qhtcp/ExpTemplate/backups/InteractTemplateB4Prompt4SDinput.R)
# * [ExpFrontend.m](templates/qhtcp/ExpTemplate/ExpFrontend.m)
# * [NotesExp1](templates/qhtcp/ExpTemplate/NotesExp1)
# * [Z_InteractionTemplate.R](templates/qhtcp/ExpTemplate/Z_InteractionTemplate.R)
# * [ZScores](templates/qhtcp/ExpTemplate/ZScores)
# * [GTAresults](templates/qhtcp/GTAresults)
# * [Exp1](templates/qhtcp/GTAresults/Exp1)
# * [Exp2](templates/qhtcp/GTAresults/Exp2)
# * [Exp3](templates/qhtcp/GTAresults/Exp3)
# * [Exp4](templates/qhtcp/GTAresults/Exp4)
# * [REMc](templates/qhtcp/REMc)
# * [AddShiftVals2.R](templates/qhtcp/REMc/AddShiftVals2.R)
# * [CompileGTF.R](templates/qhtcp/REMc/CompileGTF.R)
# * [DconJG2.py](templates/qhtcp/REMc/DconJG2.py)
# * [GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab](templates/qhtcp/REMc/GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab)
# * [GTF](templates/qhtcp/REMc/GTF)
# * [analyze_v2.pl](templates/qhtcp/REMc/GTF/analyze_v2.pl)
# * [Component](templates/qhtcp/REMc/GTF/Component)
# * [analyze_v2.pl](templates/qhtcp/REMc/GTF/Component/analyze_v2.pl)
# * [Concatenate_GTF_results.py](templates/qhtcp/REMc/GTF/Component/Concatenate_GTF_results.py)
# * [gene_association.sgd](templates/qhtcp/REMc/GTF/Component/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/REMc/GTF/Component/gene_ontology_edit.obo)
# * [ORF_List_DAmPs_Only.txt](templates/qhtcp/REMc/GTF/Component/ORF_List_DAmPs_Only.txt)
# * [ORF_List_Without_DAmPs.txt](templates/qhtcp/REMc/GTF/Component/ORF_List_Without_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/REMc/GTF/Component/ORFs_w_DAmP_list.txt)
# * [SGD_features.tab](templates/qhtcp/REMc/GTF/Component/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/REMc/GTF/Component/SGD_features.tab.txt)
# * [terms2tsv_v4.pl](templates/qhtcp/REMc/GTF/Component/terms2tsv_v4.pl)
# * [Concatenate_GTF_results.py](templates/qhtcp/REMc/GTF/Concatenate_GTF_results.py)
# * [Function](templates/qhtcp/REMc/GTF/Function)
# * [analyze_v2.pl](templates/qhtcp/REMc/GTF/Function/analyze_v2.pl)
# * [Concatenate_GTF_results.py](templates/qhtcp/REMc/GTF/Function/Concatenate_GTF_results.py)
# * [gene_association.sgd](templates/qhtcp/REMc/GTF/Function/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/REMc/GTF/Function/gene_ontology_edit.obo)
# * [ORF_List_DAmPs_Only.txt](templates/qhtcp/REMc/GTF/Function/ORF_List_DAmPs_Only.txt)
# * [ORF_List_Without_DAmPs.txt](templates/qhtcp/REMc/GTF/Function/ORF_List_Without_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/REMc/GTF/Function/ORFs_w_DAmP_list.txt)
# * [SGD_features.tab](templates/qhtcp/REMc/GTF/Function/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/REMc/GTF/Function/SGD_features.tab.txt)
# * [terms2tsv_v4.pl](templates/qhtcp/REMc/GTF/Function/terms2tsv_v4.pl)
# * [gene_association.sgd](templates/qhtcp/REMc/GTF/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/REMc/GTF/gene_ontology_edit.obo)
# * [GOontologyPar.sh](templates/qhtcp/REMc/GTF/GOontologyPar.sh)
# * [Process](templates/qhtcp/REMc/GTF/Process)
# * [analyze_v2.pl](templates/qhtcp/REMc/GTF/Process/analyze_v2.pl)
# * [Concatenate_GTF_results.py](templates/qhtcp/REMc/GTF/Process/Concatenate_GTF_results.py)
# * [gene_association.sgd](templates/qhtcp/REMc/GTF/Process/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/REMc/GTF/Process/gene_ontology_edit.obo)
# * [ORF_List_DAmPs_Only.txt](templates/qhtcp/REMc/GTF/Process/ORF_List_DAmPs_Only.txt)
# * [ORF_List_Without_DAmPs.txt](templates/qhtcp/REMc/GTF/Process/ORF_List_Without_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/REMc/GTF/Process/ORFs_w_DAmP_list.txt)
# * [SGD_features.tab](templates/qhtcp/REMc/GTF/Process/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/REMc/GTF/Process/SGD_features.tab.txt)
# * [terms2tsv_v4.pl](templates/qhtcp/REMc/GTF/Process/terms2tsv_v4.pl)
# * [SeanEmailPython2](templates/qhtcp/REMc/GTF/SeanEmailPython2)
# * [SGD_features.tab](templates/qhtcp/REMc/GTF/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/REMc/GTF/SGD_features.tab.txt)
# * [terms2tsv_v4.pl](templates/qhtcp/REMc/GTF/terms2tsv_v4.pl)
# * [jingyuJava_1_7_extractLib.jar](templates/qhtcp/REMc/jingyuJava_1_7_extractLib.jar)
# * [JoinInteractExps3dev.R](templates/qhtcp/REMc/JoinInteractExps3dev.R)
# * [Notes: REMc, GTF_Ontologies and Associated_Heatmaps ](templates/qhtcp/REMc/Notes: REMc, GTF_Ontologies and Associated_Heatmaps )
# * [old_orf_lists](templates/qhtcp/REMc/old_orf_lists)
# * [ORF_List_DAmPs_Only.txt](templates/qhtcp/REMc/old_orf_lists/ORF_List_DAmPs_Only.txt)
# * [ORF_List_Without_DAmPs.txt](templates/qhtcp/REMc/old_orf_lists/ORF_List_Without_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/REMc/old_orf_lists/ORFs_w_DAmP_list.txt)
# * [ORF_List_DAmPs_Only.txt](templates/qhtcp/REMc/ORF_List_DAmPs_Only.txt)
# * [ORF_List_Without_DAmPs.txt](templates/qhtcp/REMc/ORF_List_Without_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/REMc/ORFs_w_DAmP_list.txt)
# * [REMcHeatmaps](templates/qhtcp/REMc/REMcHeatmaps)
# * [REMcHeatmapsWithHomology](templates/qhtcp/REMc/REMcHeatmapsWithHomology)
# * [17_0503_DAmPs_Only.txt](templates/qhtcp/REMc/REMcHeatmapsWithHomology/17_0503_DAmPs_Only.txt)
# * [Homology](templates/qhtcp/REMc/REMcHeatmapsWithHomology/Homology)
# * [REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R](templates/qhtcp/REMc/REMcHeatmapsWithHomology/REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R)
# * [Yeast_Human_Homology_Mapping_biomaRt_18_0920.csv](templates/qhtcp/REMc/REMcHeatmapsWithHomology/Yeast_Human_Homology_Mapping_biomaRt_18_0920.csv)
# * [REMcHeatmaps_zscores.R](templates/qhtcp/REMc/REMcHeatmaps_zscores.R)
# * [REMcJava](templates/qhtcp/REMc/REMcJava)
# * [java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64)
# * [jre](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre)
# * [ASSEMBLY_EXCEPTION](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/ASSEMBLY_EXCEPTION)
# * [bin](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin)
# * [alt-java](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/alt-java)
# * [java](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/java)
# * [jjs](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/jjs)
# * [keytool](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/keytool)
# * [orbd](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/orbd)
# * [pack200](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/pack200)
# * [policytool](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/policytool)
# * [rmid](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/rmid)
# * [rmiregistry](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/rmiregistry)
# * [servertool](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/servertool)
# * [tnameserv](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/tnameserv)
# * [unpack200](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/unpack200)
# * [lib](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib)
# * [amd64](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64)
# * [client](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/client)
# * [jli](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/jli)
# * [libjli.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/jli/libjli.so)
# * [jvm.cfg](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/jvm.cfg)
# * [libattach.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libattach.so)
# * [libawt_headless.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libawt_headless.so)
# * [libawt.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libawt.so)
# * [libawt_xawt.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libawt_xawt.so)
# * [libdt_socket.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libdt_socket.so)
# * [libfontmanager.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libfontmanager.so)
# * [libhprof.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libhprof.so)
# * [libinstrument.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libinstrument.so)
# * [libj2gss.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libj2gss.so)
# * [libj2pcsc.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libj2pcsc.so)
# * [libj2pkcs11.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libj2pkcs11.so)
# * [libjaas_unix.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjaas_unix.so)
# * [libjava_crw_demo.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjava_crw_demo.so)
# * [libjavajpeg.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjavajpeg.so)
# * [libjava.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjava.so)
# * [libjawt.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjawt.so)
# * [libjdwp.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjdwp.so)
# * [libjsdt.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjsdt.so)
# * [libjsig.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjsig.so)
# * [libjsoundalsa.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjsoundalsa.so)
# * [libjsound.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjsound.so)
# * [liblcms.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/liblcms.so)
# * [libmanagement.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libmanagement.so)
# * [libmlib_image.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libmlib_image.so)
# * [libnet.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libnet.so)
# * [libnio.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libnio.so)
# * [libnpt.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libnpt.so)
# * [libsaproc.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libsaproc.so)
# * [libsctp.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libsctp.so)
# * [libsplashscreen.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libsplashscreen.so)
# * [libsunec.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libsunec.so)
# * [libunpack.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libunpack.so)
# * [libverify.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libverify.so)
# * [libzip.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libzip.so)
# * [server](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/server)
# * [classes.jsa](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/server/classes.jsa)
# * [libjsig.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/server/libjsig.so)
# * [libjvm.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/server/libjvm.so)
# * [Xusage.txt](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/server/Xusage.txt)
# * [applet](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/applet)
# * [calendars.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/calendars.properties)
# * [charsets.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/charsets.jar)
# * [classlist](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/classlist)
# * [cmm](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/cmm)
# * [CIEXYZ.pf](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/cmm/CIEXYZ.pf)
# * [GRAY.pf](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/cmm/GRAY.pf)
# * [LINEAR_RGB.pf](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/cmm/LINEAR_RGB.pf)
# * [PYCC.pf](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/cmm/PYCC.pf)
# * [sRGB.pf](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/cmm/sRGB.pf)
# * [content-types.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/content-types.properties)
# * [currency.data](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/currency.data)
# * [ext](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext)
# * [cldrdata.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/cldrdata.jar)
# * [dnsns.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/dnsns.jar)
# * [jaccess.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/jaccess.jar)
# * [localedata.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/localedata.jar)
# * [meta-index](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/meta-index)
# * [nashorn.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/nashorn.jar)
# * [sunec.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/sunec.jar)
# * [sunjce_provider.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/sunjce_provider.jar)
# * [sunpkcs11.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/sunpkcs11.jar)
# * [zipfs.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/zipfs.jar)
# * [flavormap.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/flavormap.properties)
# * [hijrah-config-umalqura.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/hijrah-config-umalqura.properties)
# * [images](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images)
# * [cursors](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors)
# * [cursors.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/cursors.properties)
# * [invalid32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/invalid32x32.gif)
# * [motif_CopyDrop32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/motif_CopyDrop32x32.gif)
# * [motif_CopyNoDrop32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/motif_CopyNoDrop32x32.gif)
# * [motif_LinkDrop32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/motif_LinkDrop32x32.gif)
# * [motif_LinkNoDrop32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/motif_LinkNoDrop32x32.gif)
# * [motif_MoveDrop32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/motif_MoveDrop32x32.gif)
# * [motif_MoveNoDrop32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/motif_MoveNoDrop32x32.gif)
# * [jce.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jce.jar)
# * [jexec](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jexec)
# * [jfr](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jfr)
# * [default.jfc](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jfr/default.jfc)
# * [profile.jfc](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jfr/profile.jfc)
# * [jfr.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jfr.jar)
# * [jsse.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jsse.jar)
# * [jvm.hprof.txt](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jvm.hprof.txt)
# * [logging.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/logging.properties)
# * [management](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/management)
# * [jmxremote.access](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/management/jmxremote.access)
# * [jmxremote.password.template](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/management/jmxremote.password.template)
# * [management.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/management/management.properties)
# * [snmp.acl.template](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/management/snmp.acl.template)
# * [management-agent.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/management-agent.jar)
# * [meta-index](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/meta-index)
# * [net.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/net.properties)
# * [psfontj2d.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/psfontj2d.properties)
# * [psfont.properties.ja](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/psfont.properties.ja)
# * [resources.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/resources.jar)
# * [rt.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/rt.jar)
# * [security](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security)
# * [blacklisted.certs](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/blacklisted.certs)
# * [cacerts](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/cacerts)
# * [java.policy](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/java.policy)
# * [java.security](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/java.security)
# * [nss.cfg](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/nss.cfg)
# * [policy](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy)
# * [limited](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy/limited)
# * [local_policy.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy/limited/local_policy.jar)
# * [US_export_policy.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy/limited/US_export_policy.jar)
# * [unlimited](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy/unlimited)
# * [local_policy.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy/unlimited/local_policy.jar)
# * [US_export_policy.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy/unlimited/US_export_policy.jar)
# * [sound.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/sound.properties)
# * [tzdb.dat](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/tzdb.dat)
# * [LICENSE](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/LICENSE)
# * [THIRD_PARTY_README](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/THIRD_PARTY_README)
# * [TermSpecificHeatmaps](templates/qhtcp/TermSpecificHeatmaps)
# #
# As stated earlier, the user can add folders to back up temporary results, study-related notes, or other related work. # As stated earlier, the user can add folders to back up temporary results, study-related notes, or other related work.
# However, it is advised to set up and use separate STUDIES when evaluating differing data sets whether that is from experiment results files or from differing data selections in the first interaction … .R script stage. # However, it is advised to set up and use separate STUDIES when evaluating differing data sets whether that is from experiment results files or from differing data selections in the first interaction … .R script stage.
@@ -982,7 +683,6 @@ qhtcp() {
done done
# Run remc as part of the QHTCP process # Run remc as part of the QHTCP process
remc remc
} }
@@ -1043,29 +743,88 @@ gtf() {
module gta module gta
# @section GTA # @section GTA
# @description GTA module for QHTCP # @description GTA module for QHTCP
# TODO # NOTES
# * Heavily modified GTAtemplate.R # * Heavily modified GTAtemplate.R
# TODO
# * # *
# *
# @set GTA_OUT_DIR string The GTA output results dir
# @set all_sgd_terms_csv string The all_SGD_GOTerms_for_QHTCPtk.csv file
# @set sgd_terms_tfile string The go_terms.tab file
# @set sgd_features_file string The gene_association.sgd file
# @set gene_ontology_file string The gene_ontology_edit.obo file
# @set zscores_file string The ZScores_interaction.csv file
gta() { gta() {
debug "Running: ${FUNCNAME[0]}" debug "Running: ${FUNCNAME[0]}"
GTA_OUT_DIR="$QHTCP_PROJECT_DIR/GTAresults"
all_sgd_terms_csv="$CODE_DIR/All_SGD_GOTerms_for_QHTCPtk.csv"
sgd_terms_tfile="$CODE_DIR/go_terms.tab" sgd_terms_tfile="$CODE_DIR/go_terms.tab"
sgd_features_file="$CODE_DIR/gene_association.sgd" sgd_features_file="$CODE_DIR/gene_association.sgd"
gta_out_dir="$QHTCP_PROJECT_DIR/GTAresults" gene_ontology_file="$CODE_DIR/gene_ontology_edit.obo"
zscores_file="ZScores/ZScores_Interaction.csv"
# Sets STUDIES_NUM and NUM_STUDIES # Sets STUDIES_NUM and NUM_STUDIES
get_studies get_studies
[[ -d $gta_out_dir ]] || mkdir "$gta_out_dir" [[ -d $GTA_OUT_DIR ]] || mkdir "$GTA_OUT_DIR"
# Loop over studies # Loop over the array and create pairwise arrays
for ((i=0; i<${#STUDIES_NUMS[@]}; i++)); do
for ((j=i+1; j<${#STUDIES_NUMS[@]}; j++)); do
pair=("${STUDIES_NUMS[i]}" "${STUDIES_NUMS[j]}")
echo "${pair[@]}"
done
done
# Create unique parwise combinations of study nums from dir names
study_combos=()
for ((i=0; i<${#STUDIES_NUMS[@]}; i++)); do
# Loop through the array again
for ((j=0; j<${#STUDIES_NUMS[@]}; j++)); do
# If the indices are not the same
if [ "$i" != "$j" ]; then
# Print the unique combination
study_combos+=("${STUDIES_NUMS[$i]},${STUDIES_NUMS[$j]}")
fi
done
done
# The following are three types of studies
# Individual studies
for s in "${STUDIES_NUMS[@]}"; do for s in "${STUDIES_NUMS[@]}"; do
zscores_file="$QHTCP_PROJECT_DIR/Exp$s/ZScores/ZScores_Interaction.csv" zscores_file="$QHTCP_PROJECT_DIR/Exp$s/$zscores_file"
if [[ -f $zscores_file ]]; then if [[ -f $zscores_file ]]; then
mkdir "$gta_out_dir/Exp$s" mkdir "$GTA_OUT_DIR/Exp$s"
r_gta "Exp$s" "$zscores_file" "$sgd_terms_tfile" "$sgd_features_file" "$gta_out_dir" r_gta "Exp$s" "$zscores_file" "$sgd_terms_tfile" "$sgd_features_file" "$GTA_OUT_DIR"
fi fi
done done
# Combination studies (for pairwise comparisons)
for combo in "${study_combos[@]}"; do
# Split on comma and assign to array
IFS=',' read -ra studies <<< "$combo"
r_gta_pairwiselk "${studies[0]}" "${studies[1]}" "$STUDY_INFO_FILE" "$GTA_OUT_DIR"
done
# All studies
# If you have an unknown # of studies it must be passed last and any preceding arguments
# are required
#
#
#
#
r_gta_heatmaps \
"$STUDY_INFO_FILE" \
"$gene_ontology_file" \
"$sgd_terms_tfile" \
"$all_sgd_terms_csv" \
"$zscores_file" \
"$QHTCP_PROJECT_DIR" \
"$QHTCP_PROJECT_DIR/TermSpecificHeatmaps" \
"${STUDIES_NUMS[@]}"
} }
@@ -1110,6 +869,88 @@ r_gta() {
script="$CODE_DIR/GTAtemplate.R" script="$CODE_DIR/GTAtemplate.R"
[[ -d $5 ]] || mkdir -p "$5"
debug "$RSCRIPT $script $*"
"$RSCRIPT" "$script" "$@"
}
submodule r_gta_pairwiselk
# @description PairwiseLK.R R script
# TODO:
# * Should move directory creation from PairwiseLK.R to gta module
#
# Files:
# *
# *
#
# Output:
# *
#
# This submodule:
# * Will perform both L and K comparisons for the specified experiment folders.
# * The code uses the naming convention of PairwiseCompare_Exp’#’-Exp’#’ to standardize and keep simple the structural naming (where ‘X’ is either K or L and ‘Y’ is the number of the experiment GTA results to be found in ../GTAresult/Exp_).
# * {FYI There are also individual scripts that just do the ‘L’ or ‘K’ pairwise studies in the ../Code folder.}
#
# @arg $1 string First Exp# name
# @arg $2 string Second Exp# name
# @arg $3 string StudyInfo.txt file
# @arg $4 string output directory
#
r_gta_pairwiselk() {
debug "Running: ${FUNCNAME[0]}"
cat <<-EOF
EOF
script="$CODE_DIR/PairwiseLK.R"
[[ -d $4 ]] || mkdir -p "$4"
debug "$RSCRIPT $script $*"
"$RSCRIPT" "$script" "$@"
}
submodule r_gta_heatmaps
# @description TSHeatmaps5dev2.R R script
# TODO:
# * Script could use rename
# * Script should be refactored to automatically allow more studies
# * Script should be refactored with more looping to reduce verbosity
#
# Files:
# *
# *
#
# Output:
# *
#
# This submodule:
# * The Term Specific Heatmaps are produced directly from the ../ExpStudy/Exp_/ZScores/ZScores_Interaction.csv file generated by the user modified interaction… .R script.
# * The heatmap labeling is per the names the user wrote into the StudyInfo.txt spreadsheet.
# * Verify that the All_SGD_GOTerms_for_QHTCPtk.csv found in ../Code is what you wish to use or if you wish to use a custom modified version.
# * If you wish to use a custom modified version, create it and modify the TSHeatmaps template script (TSHeatmaps5dev2.R) and save it as a ‘TSH_study specific name’.
#
# @arg $1 string StudyInfo.csv file
# @arg $2 string gene_ontology_edit.obo file
# @arg $3 string go_terms.tab file
# @arg $4 string All_SGD_GOTerms_for_QHTCPtk.csv
# @arg $5 string ZScores_interaction.csv
# @arg $6 string base directory
# @arg $7 string output directory
#
r_gta_heatmaps() {
debug "Running: ${FUNCNAME[0]}" "$@"
cat <<-EOF
EOF
script="$CODE_DIR/TSHeatmaps5dev2.R"
[[ -d $5 ]] || mkdir -p "$5"
debug "$RSCRIPT $script $*" debug "$RSCRIPT $script $*"
"$RSCRIPT" "$script" "$@" "$RSCRIPT" "$script" "$@"
} }
@@ -1452,7 +1293,7 @@ documentation() {
# Print markdown to stdout # Print markdown to stdout
((DEBUG)) && shdoc < "$SCRIPT" ((DEBUG)) && shdoc < "$SCRIPT"
# Create markdown file # Create markdown file
shdoc < "$SCRIPT" > documentation.md shdoc < "$SCRIPT" > README.md
} }
@@ -1460,6 +1301,7 @@ documentation() {
# May eventually need to add git ops # May eventually need to add git ops
# Passes on arguments # Passes on arguments
# Most variables in main() are user configurable or can be overriden by env # Most variables in main() are user configurable or can be overriden by env
# @internal
main() { main() {
debug "Running: ${FUNCNAME[0]}" "$@" debug "Running: ${FUNCNAME[0]}" "$@"
@@ -1547,3 +1389,305 @@ main() {
main "$@" main "$@"
exit $? exit $?
# We'll need everyone to
# Template:
# templates/qhtcp
# * [A_QHTCP Study Design and Notes](templates/qhtcp/A_QHTCP Study Design and Notes)
# * [A_Suggestions for system improvements.odt](templates/qhtcp/A_QHTCP Study Design and Notes/A_Suggestions for system improvements.odt)
# * [QHTCP Study Design and Notes.odt](templates/qhtcp/A_QHTCP Study Design and Notes/QHTCP Study Design and Notes.odt)
# * [Code](templates/qhtcp/Code)
# * [22_0602_Remy_DAmPsList.txt](templates/qhtcp/Code/22_0602_Remy_DAmPsList.txt)
# * [All_SGD_GOTerms.csv](templates/qhtcp/Code/All_SGD_GOTerms.csv)
# * [All_SGD_GOTerms_for_QHTCPtk.csv](templates/qhtcp/Code/All_SGD_GOTerms_for_QHTCPtk.csv)
# * [devStuff](templates/qhtcp/Code/devStuff)
# * [InteractTemplateB4fixes.R](templates/qhtcp/Code/devStuff/InteractTemplateB4fixes.R)
# * [InteractTemplateB4Prompt4SDinput.R](templates/qhtcp/Code/devStuff/InteractTemplateB4Prompt4SDinput.R)
# * [gene_association.sgd](templates/qhtcp/Code/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/Code/gene_ontology_edit.obo)
# * [go_terms.tab](templates/qhtcp/Code/go_terms.tab)
# * [GTAtemplate.R](templates/qhtcp/Code/GTAtemplate.R)
# * [ORF_List_DAmPs_Only.txt](templates/qhtcp/Code/ORF_List_DAmPs_Only.txt)
# * [ORF_List_Without_DAmPs.txt](templates/qhtcp/Code/ORF_List_Without_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/Code/ORFs_w_DAmP_list.txt)
# * [PairwiseLK.R](templates/qhtcp/Code/PairwiseLK.R)
# * [Parameters.csv](templates/qhtcp/Code/Parameters.csv)
# * [RenameFiles2.sh](templates/qhtcp/Code/RenameFiles2.sh)
# * [ScriptTemplates](templates/qhtcp/Code/ScriptTemplates)
# * [BU_Legacy](templates/qhtcp/Code/ScriptTemplates/BU_Legacy)
# * [InteractTemplate.R](templates/qhtcp/Code/ScriptTemplates/BU_Legacy/InteractTemplate.R)
# * [Concatenate_GTF_resultsB4REMcMaster2.py](templates/qhtcp/Code/ScriptTemplates/Concatenate_GTF_resultsB4REMcMaster2.py)
# * [Concatenate_GTF_results.py](templates/qhtcp/Code/ScriptTemplates/Concatenate_GTF_results.py)
# * [GTAtemplate.R](templates/qhtcp/Code/ScriptTemplates/GTAtemplate.R)
# * [InteractionTemplate230119.R](templates/qhtcp/Code/ScriptTemplates/InteractionTemplate230119.R)
# * [JoinInteractExps3dev.R](templates/qhtcp/Code/ScriptTemplates/JoinInteractExps3dev.R)
# * [JoinInteractExps.R](templates/qhtcp/Code/ScriptTemplates/JoinInteractExps.R)
# * [PairwiseK_lbl.R](templates/qhtcp/Code/ScriptTemplates/PairwiseK_lbl.R)
# * [PairwiseLK.R](templates/qhtcp/Code/ScriptTemplates/PairwiseLK.R)
# * [PairwiseL_lbl.R](templates/qhtcp/Code/ScriptTemplates/PairwiseL_lbl.R)
# * [Remy_yor_dF_correlation_study.R](templates/qhtcp/Code/ScriptTemplates/Remy_yor_dF_correlation_study.R)
# * [TSHeatmaps5dev2.R](templates/qhtcp/Code/ScriptTemplates/TSHeatmaps5dev2.R)
# * [SGD_features.tab](templates/qhtcp/Code/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/Code/SGD_features.tab.txt)
# * [SSscripts](templates/qhtcp/Code/SSscripts)
# * [18_0205_heatmaps_zscores_2SD_color_NARem_Z_lm.R](templates/qhtcp/Code/SSscripts/18_0205_heatmaps_zscores_2SD_color_NARem_Z_lm.R)
# * [22_0603_Remy_Exclude_DAmPs.R](templates/qhtcp/Code/SSscripts/22_0603_Remy_Exclude_DAmPs.R)
# * [cmd_Doxo_SumZScore_Z_lm_Interaction_drug_all_rm_onedrug_V4_yor1_with_Dox_validationedit.R](templates/qhtcp/Code/SSscripts/cmd_Doxo_SumZScore_Z_lm_Interaction_drug_all_rm_onedrug_V4_yor1_with_Dox_validationedit.R)
# * [cmd_ScoreAllGOTerms_From_Z_lm_V2.R](templates/qhtcp/Code/SSscripts/cmd_ScoreAllGOTerms_From_Z_lm_V2.R)
# * [Compare_GTF_Averages_BetweenScreens_lm_Kvals_v2.R](templates/qhtcp/Code/SSscripts/Compare_GTF_Averages_BetweenScreens_lm_Kvals_v2.R)
# * [Compare_GTF_Averages_BetweenScreens_lm_Lvals_v2.R](templates/qhtcp/Code/SSscripts/Compare_GTF_Averages_BetweenScreens_lm_Lvals_v2.R)
# * [Compare_GTF_Averages_BetweenScreens_lm_v2.R](templates/qhtcp/Code/SSscripts/Compare_GTF_Averages_BetweenScreens_lm_v2.R)
# * [GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_3terms_V2.R](templates/qhtcp/Code/SSscripts/GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_3terms_V2.R)
# * [GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_4terms_aging.R](templates/qhtcp/Code/SSscripts/GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_4terms_aging.R)
# * [GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_4terms_v2.R](templates/qhtcp/Code/SSscripts/GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_4terms_v2.R)
# * [GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_5terms_V2.R](templates/qhtcp/Code/SSscripts/GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_5terms_V2.R)
# * [GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_V2.R](templates/qhtcp/Code/SSscripts/GO_list_All_ChildTerms_lmZscore_max100child_Heatmaps_V2.R)
# * [ScoreAllGOTerms_From_Z_lm_V2.R](templates/qhtcp/Code/SSscripts/ScoreAllGOTerms_From_Z_lm_V2.R)
# * [StudyInfo.csv](templates/qhtcp/Code/StudyInfo.csv)
# * [TSHeatmaps5dev2.R](templates/qhtcp/Code/TSHeatmaps5dev2.R)
# * [Updating files](templates/qhtcp/Code/Updating files)
# * [23_0929](templates/qhtcp/Code/Updating files/23_0929)
# * [gene_association.sgd](templates/qhtcp/Code/Updating files/23_0929/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/Code/Updating files/23_0929/gene_ontology_edit.obo)
# * [go_terms.tab](templates/qhtcp/Code/Updating files/23_0929/go_terms.tab)
# * [ORFs_NO_DAmPs.txt](templates/qhtcp/Code/Updating files/23_0929/ORFs_NO_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/Code/Updating files/23_0929/ORFs_w_DAmP_list.txt)
# * [SGD_features.tab](templates/qhtcp/Code/Updating files/23_0929/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/Code/Updating files/23_0929/SGD_features.tab.txt)
# * [original_outdated](templates/qhtcp/Code/Updating files/original_outdated)
# * [gene_association.sgd](templates/qhtcp/Code/Updating files/original_outdated/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/Code/Updating files/original_outdated/gene_ontology_edit.obo)
# * [go_terms.tab](templates/qhtcp/Code/Updating files/original_outdated/go_terms.tab)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/Code/Updating files/original_outdated/ORFs_w_DAmP_list.txt)
# * [SGD_features.tab](templates/qhtcp/Code/Updating files/original_outdated/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/Code/Updating files/original_outdated/SGD_features.tab.txt)
# * [SGDFeatureUpdates](templates/qhtcp/Code/Updating files/SGDFeatureUpdates)
# * [23_0927_SGDFeatures for KO.DAmP_library.csv](templates/qhtcp/Code/Updating files/SGDFeatureUpdates/23_0927_SGDFeatures for KO.DAmP_library.csv)
# * [23_0927_SGDFeatures for KO.DAmP_library.tsv](templates/qhtcp/Code/Updating files/SGDFeatureUpdates/23_0927_SGDFeatures for KO.DAmP_library.tsv)
# * [copy of original files before updates](templates/qhtcp/Code/Updating files/SGDFeatureUpdates/copy of original files before updates)
# * [SGD_features.tab_updates.xlsx](templates/qhtcp/Code/Updating files/SGDFeatureUpdates/SGD_features.tab_updates.xlsx)
# * [SGD_features_UPDATES for 2 files.xlsx](templates/qhtcp/Code/Updating files/SGDFeatureUpdates/SGD_features_UPDATES for 2 files.xlsx)
# * [SGD readme files](templates/qhtcp/Code/Updating files/SGD readme files)
# * [gene_association.README](templates/qhtcp/Code/Updating files/SGD readme files/gene_association.README)
# * [go_terms.README](templates/qhtcp/Code/Updating files/SGD readme files/go_terms.README)
# * [_Updating_Notes_23_0329.txt](templates/qhtcp/Code/Updating files/_Updating_Notes_23_0329.txt)
# * [Updating Q-HTCP_SourceFiles.docx](templates/qhtcp/Code/Updating files/Updating Q-HTCP_SourceFiles.docx)
# * [Documentation](templates/qhtcp/Documentation)
# * [20_0329_SS_Q_HTCP_Analysis_Readme.docx](templates/qhtcp/Documentation/20_0329_SS_Q_HTCP_Analysis_Readme.docx)
# * [Jingyu_REMc_Instruction for clustering and heatmap plotting _updated2013Mar.docx](templates/qhtcp/Documentation/Jingyu_REMc_Instruction for clustering and heatmap plotting _updated2013Mar.docx)
# * [ExpTemplate](templates/qhtcp/ExpTemplate)
# * [backups](templates/qhtcp/ExpTemplate/backups)
# * [InteractTemplateB4Prompt4SDinput.R](templates/qhtcp/ExpTemplate/backups/InteractTemplateB4Prompt4SDinput.R)
# * [ExpFrontend.m](templates/qhtcp/ExpTemplate/ExpFrontend.m)
# * [NotesExp1](templates/qhtcp/ExpTemplate/NotesExp1)
# * [Z_InteractionTemplate.R](templates/qhtcp/ExpTemplate/Z_InteractionTemplate.R)
# * [ZScores](templates/qhtcp/ExpTemplate/ZScores)
# * [GTAresults](templates/qhtcp/GTAresults)
# * [Exp1](templates/qhtcp/GTAresults/Exp1)
# * [Exp2](templates/qhtcp/GTAresults/Exp2)
# * [Exp3](templates/qhtcp/GTAresults/Exp3)
# * [Exp4](templates/qhtcp/GTAresults/Exp4)
# * [REMc](templates/qhtcp/REMc)
# * [AddShiftVals2.R](templates/qhtcp/REMc/AddShiftVals2.R)
# * [CompileGTF.R](templates/qhtcp/REMc/CompileGTF.R)
# * [DconJG2.py](templates/qhtcp/REMc/DconJG2.py)
# * [GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab](templates/qhtcp/REMc/GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab)
# * [GTF](templates/qhtcp/REMc/GTF)
# * [analyze_v2.pl](templates/qhtcp/REMc/GTF/analyze_v2.pl)
# * [Component](templates/qhtcp/REMc/GTF/Component)
# * [analyze_v2.pl](templates/qhtcp/REMc/GTF/Component/analyze_v2.pl)
# * [Concatenate_GTF_results.py](templates/qhtcp/REMc/GTF/Component/Concatenate_GTF_results.py)
# * [gene_association.sgd](templates/qhtcp/REMc/GTF/Component/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/REMc/GTF/Component/gene_ontology_edit.obo)
# * [ORF_List_DAmPs_Only.txt](templates/qhtcp/REMc/GTF/Component/ORF_List_DAmPs_Only.txt)
# * [ORF_List_Without_DAmPs.txt](templates/qhtcp/REMc/GTF/Component/ORF_List_Without_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/REMc/GTF/Component/ORFs_w_DAmP_list.txt)
# * [SGD_features.tab](templates/qhtcp/REMc/GTF/Component/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/REMc/GTF/Component/SGD_features.tab.txt)
# * [terms2tsv_v4.pl](templates/qhtcp/REMc/GTF/Component/terms2tsv_v4.pl)
# * [Concatenate_GTF_results.py](templates/qhtcp/REMc/GTF/Concatenate_GTF_results.py)
# * [Function](templates/qhtcp/REMc/GTF/Function)
# * [analyze_v2.pl](templates/qhtcp/REMc/GTF/Function/analyze_v2.pl)
# * [Concatenate_GTF_results.py](templates/qhtcp/REMc/GTF/Function/Concatenate_GTF_results.py)
# * [gene_association.sgd](templates/qhtcp/REMc/GTF/Function/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/REMc/GTF/Function/gene_ontology_edit.obo)
# * [ORF_List_DAmPs_Only.txt](templates/qhtcp/REMc/GTF/Function/ORF_List_DAmPs_Only.txt)
# * [ORF_List_Without_DAmPs.txt](templates/qhtcp/REMc/GTF/Function/ORF_List_Without_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/REMc/GTF/Function/ORFs_w_DAmP_list.txt)
# * [SGD_features.tab](templates/qhtcp/REMc/GTF/Function/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/REMc/GTF/Function/SGD_features.tab.txt)
# * [terms2tsv_v4.pl](templates/qhtcp/REMc/GTF/Function/terms2tsv_v4.pl)
# * [gene_association.sgd](templates/qhtcp/REMc/GTF/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/REMc/GTF/gene_ontology_edit.obo)
# * [GOontologyPar.sh](templates/qhtcp/REMc/GTF/GOontologyPar.sh)
# * [Process](templates/qhtcp/REMc/GTF/Process)
# * [analyze_v2.pl](templates/qhtcp/REMc/GTF/Process/analyze_v2.pl)
# * [Concatenate_GTF_results.py](templates/qhtcp/REMc/GTF/Process/Concatenate_GTF_results.py)
# * [gene_association.sgd](templates/qhtcp/REMc/GTF/Process/gene_association.sgd)
# * [gene_ontology_edit.obo](templates/qhtcp/REMc/GTF/Process/gene_ontology_edit.obo)
# * [ORF_List_DAmPs_Only.txt](templates/qhtcp/REMc/GTF/Process/ORF_List_DAmPs_Only.txt)
# * [ORF_List_Without_DAmPs.txt](templates/qhtcp/REMc/GTF/Process/ORF_List_Without_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/REMc/GTF/Process/ORFs_w_DAmP_list.txt)
# * [SGD_features.tab](templates/qhtcp/REMc/GTF/Process/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/REMc/GTF/Process/SGD_features.tab.txt)
# * [terms2tsv_v4.pl](templates/qhtcp/REMc/GTF/Process/terms2tsv_v4.pl)
# * [SeanEmailPython2](templates/qhtcp/REMc/GTF/SeanEmailPython2)
# * [SGD_features.tab](templates/qhtcp/REMc/GTF/SGD_features.tab)
# * [SGD_features.tab.txt](templates/qhtcp/REMc/GTF/SGD_features.tab.txt)
# * [terms2tsv_v4.pl](templates/qhtcp/REMc/GTF/terms2tsv_v4.pl)
# * [jingyuJava_1_7_extractLib.jar](templates/qhtcp/REMc/jingyuJava_1_7_extractLib.jar)
# * [JoinInteractExps3dev.R](templates/qhtcp/REMc/JoinInteractExps3dev.R)
# * [Notes: REMc, GTF_Ontologies and Associated_Heatmaps ](templates/qhtcp/REMc/Notes: REMc, GTF_Ontologies and Associated_Heatmaps )
# * [old_orf_lists](templates/qhtcp/REMc/old_orf_lists)
# * [ORF_List_DAmPs_Only.txt](templates/qhtcp/REMc/old_orf_lists/ORF_List_DAmPs_Only.txt)
# * [ORF_List_Without_DAmPs.txt](templates/qhtcp/REMc/old_orf_lists/ORF_List_Without_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/REMc/old_orf_lists/ORFs_w_DAmP_list.txt)
# * [ORF_List_DAmPs_Only.txt](templates/qhtcp/REMc/ORF_List_DAmPs_Only.txt)
# * [ORF_List_Without_DAmPs.txt](templates/qhtcp/REMc/ORF_List_Without_DAmPs.txt)
# * [ORFs_w_DAmP_list.txt](templates/qhtcp/REMc/ORFs_w_DAmP_list.txt)
# * [REMcHeatmaps](templates/qhtcp/REMc/REMcHeatmaps)
# * [REMcHeatmapsWithHomology](templates/qhtcp/REMc/REMcHeatmapsWithHomology)
# * [17_0503_DAmPs_Only.txt](templates/qhtcp/REMc/REMcHeatmapsWithHomology/17_0503_DAmPs_Only.txt)
# * [Homology](templates/qhtcp/REMc/REMcHeatmapsWithHomology/Homology)
# * [REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R](templates/qhtcp/REMc/REMcHeatmapsWithHomology/REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R)
# * [Yeast_Human_Homology_Mapping_biomaRt_18_0920.csv](templates/qhtcp/REMc/REMcHeatmapsWithHomology/Yeast_Human_Homology_Mapping_biomaRt_18_0920.csv)
# * [REMcHeatmaps_zscores.R](templates/qhtcp/REMc/REMcHeatmaps_zscores.R)
# * [REMcJava](templates/qhtcp/REMc/REMcJava)
# * [java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64)
# * [jre](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre)
# * [ASSEMBLY_EXCEPTION](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/ASSEMBLY_EXCEPTION)
# * [bin](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin)
# * [alt-java](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/alt-java)
# * [java](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/java)
# * [jjs](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/jjs)
# * [keytool](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/keytool)
# * [orbd](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/orbd)
# * [pack200](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/pack200)
# * [policytool](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/policytool)
# * [rmid](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/rmid)
# * [rmiregistry](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/rmiregistry)
# * [servertool](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/servertool)
# * [tnameserv](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/tnameserv)
# * [unpack200](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/unpack200)
# * [lib](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib)
# * [amd64](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64)
# * [client](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/client)
# * [jli](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/jli)
# * [libjli.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/jli/libjli.so)
# * [jvm.cfg](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/jvm.cfg)
# * [libattach.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libattach.so)
# * [libawt_headless.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libawt_headless.so)
# * [libawt.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libawt.so)
# * [libawt_xawt.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libawt_xawt.so)
# * [libdt_socket.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libdt_socket.so)
# * [libfontmanager.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libfontmanager.so)
# * [libhprof.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libhprof.so)
# * [libinstrument.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libinstrument.so)
# * [libj2gss.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libj2gss.so)
# * [libj2pcsc.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libj2pcsc.so)
# * [libj2pkcs11.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libj2pkcs11.so)
# * [libjaas_unix.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjaas_unix.so)
# * [libjava_crw_demo.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjava_crw_demo.so)
# * [libjavajpeg.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjavajpeg.so)
# * [libjava.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjava.so)
# * [libjawt.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjawt.so)
# * [libjdwp.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjdwp.so)
# * [libjsdt.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjsdt.so)
# * [libjsig.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjsig.so)
# * [libjsoundalsa.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjsoundalsa.so)
# * [libjsound.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libjsound.so)
# * [liblcms.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/liblcms.so)
# * [libmanagement.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libmanagement.so)
# * [libmlib_image.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libmlib_image.so)
# * [libnet.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libnet.so)
# * [libnio.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libnio.so)
# * [libnpt.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libnpt.so)
# * [libsaproc.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libsaproc.so)
# * [libsctp.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libsctp.so)
# * [libsplashscreen.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libsplashscreen.so)
# * [libsunec.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libsunec.so)
# * [libunpack.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libunpack.so)
# * [libverify.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libverify.so)
# * [libzip.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/libzip.so)
# * [server](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/server)
# * [classes.jsa](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/server/classes.jsa)
# * [libjsig.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/server/libjsig.so)
# * [libjvm.so](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/server/libjvm.so)
# * [Xusage.txt](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/amd64/server/Xusage.txt)
# * [applet](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/applet)
# * [calendars.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/calendars.properties)
# * [charsets.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/charsets.jar)
# * [classlist](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/classlist)
# * [cmm](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/cmm)
# * [CIEXYZ.pf](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/cmm/CIEXYZ.pf)
# * [GRAY.pf](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/cmm/GRAY.pf)
# * [LINEAR_RGB.pf](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/cmm/LINEAR_RGB.pf)
# * [PYCC.pf](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/cmm/PYCC.pf)
# * [sRGB.pf](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/cmm/sRGB.pf)
# * [content-types.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/content-types.properties)
# * [currency.data](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/currency.data)
# * [ext](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext)
# * [cldrdata.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/cldrdata.jar)
# * [dnsns.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/dnsns.jar)
# * [jaccess.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/jaccess.jar)
# * [localedata.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/localedata.jar)
# * [meta-index](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/meta-index)
# * [nashorn.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/nashorn.jar)
# * [sunec.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/sunec.jar)
# * [sunjce_provider.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/sunjce_provider.jar)
# * [sunpkcs11.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/sunpkcs11.jar)
# * [zipfs.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/ext/zipfs.jar)
# * [flavormap.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/flavormap.properties)
# * [hijrah-config-umalqura.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/hijrah-config-umalqura.properties)
# * [images](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images)
# * [cursors](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors)
# * [cursors.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/cursors.properties)
# * [invalid32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/invalid32x32.gif)
# * [motif_CopyDrop32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/motif_CopyDrop32x32.gif)
# * [motif_CopyNoDrop32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/motif_CopyNoDrop32x32.gif)
# * [motif_LinkDrop32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/motif_LinkDrop32x32.gif)
# * [motif_LinkNoDrop32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/motif_LinkNoDrop32x32.gif)
# * [motif_MoveDrop32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/motif_MoveDrop32x32.gif)
# * [motif_MoveNoDrop32x32.gif](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/images/cursors/motif_MoveNoDrop32x32.gif)
# * [jce.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jce.jar)
# * [jexec](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jexec)
# * [jfr](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jfr)
# * [default.jfc](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jfr/default.jfc)
# * [profile.jfc](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jfr/profile.jfc)
# * [jfr.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jfr.jar)
# * [jsse.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jsse.jar)
# * [jvm.hprof.txt](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/jvm.hprof.txt)
# * [logging.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/logging.properties)
# * [management](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/management)
# * [jmxremote.access](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/management/jmxremote.access)
# * [jmxremote.password.template](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/management/jmxremote.password.template)
# * [management.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/management/management.properties)
# * [snmp.acl.template](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/management/snmp.acl.template)
# * [management-agent.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/management-agent.jar)
# * [meta-index](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/meta-index)
# * [net.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/net.properties)
# * [psfontj2d.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/psfontj2d.properties)
# * [psfont.properties.ja](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/psfont.properties.ja)
# * [resources.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/resources.jar)
# * [rt.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/rt.jar)
# * [security](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security)
# * [blacklisted.certs](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/blacklisted.certs)
# * [cacerts](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/cacerts)
# * [java.policy](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/java.policy)
# * [java.security](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/java.security)
# * [nss.cfg](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/nss.cfg)
# * [policy](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy)
# * [limited](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy/limited)
# * [local_policy.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy/limited/local_policy.jar)
# * [US_export_policy.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy/limited/US_export_policy.jar)
# * [unlimited](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy/unlimited)
# * [local_policy.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy/unlimited/local_policy.jar)
# * [US_export_policy.jar](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/security/policy/unlimited/US_export_policy.jar)
# * [sound.properties](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/sound.properties)
# * [tzdb.dat](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/lib/tzdb.dat)
# * [LICENSE](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/LICENSE)
# * [THIRD_PARTY_README](templates/qhtcp/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/THIRD_PARTY_README)
# * [TermSpecificHeatmaps](templates/qhtcp/TermSpecificHeatmaps)

84
workflow/templates/qhtcp/Code/PairwiseLK.R
View File

@@ -1,41 +1,67 @@
#4.This R script performs GTA L and K Pairwise Compares for user specified pairs of Experiments #!/usr/bin/env Rscript
#Arg1 is the first Experiment or a user ordered pair (i.e., Exp3) # This R script performs GTA L and K Pairwise Compares for user specified pairs of Experiments
#Arg2 is the second Experiment or a user ordered pair (i.e., Exp4) #
#Note user can put whatever names they wish for the Canonical Exp1..4 in the ../Code/ExpLabels.txt spread sheet # Updated 240724 Bryan C Roessler to improve file operations and portability
#which correlates the canonical Exp Name with the user stylized label for plots and output files. # NOTE: The two required arguments are the same and now there are two optional arguments
# 1. Exp1
# 2. Exp2
# 3. StudyInfo.csv file
# 4. Output Directory
library("ggplot2")
library("plotly")
library("htmlwidgets")
library("extrafont")
library("grid")
library("ggthemes")
library(ggplot2) args <- commandArgs(TRUE)
library(plotly) exp_name <- args[1]
library(htmlwidgets) exp_name2 <- args[2]
library(extrafont)
library(grid)
library(ggthemes)
Args <- commandArgs(TRUE)
expNm= Args[1] #i.e., "Exp3" if (length(args) > 3) {
expNm[2]= Args[2] #i.e., "Exp4" study_info_file <- args[3]
expNumber1<- as.numeric(sub("^.*?(\\d+)$", "\\1", expNm[1])) } else {
expNumber2<- as.numeric(sub("^.*?(\\d+)$", "\\1", expNm[2])) study_info_file <- "StudyInfo.csv"
#labels <- read.delim("ExpLabels.txt",skip=0,as.is=T,row.names=1,strip.white=TRUE) }
#labels <- read.delim("StudyInfo.csv",skip=0,as.is=T,row.names=1,strip.white=TRUE)
Labels<- read.csv(file= "StudyInfo.csv",stringsAsFactors = FALSE)
Name1 <- Labels[expNumber1,2] #ssArg2 These are now supplied by Code/ExpLabels.csv which is user edited
Name2 <- Labels[expNumber2,2] #ssArg4
Wstudy= getwd()
input_file1 <- paste0("../GTAresults/",expNm[1],"/Average_GOTerms_All.csv" ) #Args[1]
input_file2 <- paste0("../GTAresults/",expNm[2],"/Average_GOTerms_All.csv" ) #Args[3]
pairDirL= paste0("../GTAresults/","PairwiseCompareL_",expNm[1],"-",expNm[2]) if (length(args) > 4) {
pairDirK= paste0("../GTAresults/","PairwiseCompareK_",expNm[1],"-",expNm[2]) output_dir <- args[4]
outPathGTAcompare= "../GTAresults/PairwiseCompareL" #paste0(Wstudy,"/GTAresults/PairwiseCompareL) } else {
outPathGTAcompare[2]= "../GTAresults/PairwiseCompareK" #paste0(Wstudy,"/GTAresults/PairwiseCompareK") output_dir <- "../GTAresults"
}
# if (length(args) > 3) {
# sgd_terms_file <- args[3]
# } else {
# sgd_terms_file <- "../Code/go_terms.tab"
# }
# if (length(args) > 4) {
# sgd_features_file <- args[4]
# } else {
# sgd_features_file <- "../Code/gene_association.sgd"
# }
expNumber1<- as.numeric(sub("^.*?(\\d+)$", "\\1", exp_name))
expNumber2<- as.numeric(sub("^.*?(\\d+)$", "\\1", exp_name2))
Labels<- read.csv(file=study_info_file,stringsAsFactors = FALSE)
Name1 <- Labels[expNumber1,2]
Name2 <- Labels[expNumber2,2]
go_terms_file <- "Average_GOTerms_All.csv"
input_file1 <- file.path(output_dir,exp_name,go_terms_file)
input_file2 <- file.path(output_dir,exp_name2,go_terms_file)
pairDirL= file.path(output_dir,"PairwiseCompareL_",exp_name,"-",exp_name2)
pairDirK= file.path(output_dir,"PairwiseCompareK_",exp_name,"-",exp_name2)
outPathGTAcompare= file.path(output_dir,"PairwiseCompareL")
outPathGTAcompare[2]= file.path(output_dir,"PairwiseCompareK")
#dir.create(outPathGTAcompare[1]) #dir.create(outPathGTAcompare[1])
dir.create(pairDirL) #(outPathGTAcompare[1]) dir.create(pairDirL) #(outPathGTAcompare[1])
dir.create(pairDirK) #(outPathGTAcompare[2]) dir.create(pairDirK) #(outPathGTAcompare[2])
###########BEGIN PAIRWISE L-----LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL ###########BEGIN PAIRWISE L-----LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
#define the output path (as fourth argument from Rscript)
outputpath <- pairDirL #outPathGTAcompare[1] #Args[5] outputpath <- pairDirL #outPathGTAcompare[1] #Args[5]
#outputPlotly <- "../GTAresults/PairwiseCompareL/" #"/GTAresults/PairwiseCompareL/" #outputPlotly <- "../GTAresults/PairwiseCompareL/" #"/GTAresults/PairwiseCompareL/"
print("39") print("39")

205
workflow/templates/qhtcp/Code/TSHeatmaps5dev2.R
View File

@@ -1,3 +1,16 @@
#!/usr/bin/env Rscript
# Makes heat maps of multiple experiments
#
# Updated 240724 Bryan C Roessler to improve file operations and portability
# I tried to leave as much logic intact as possible, just feeding in vars in a better way
# NOTE: The script now has 7 required arguments and a variable number of input experiments
# @arg $1 string StudyInfo.csv file
# @arg $2 string gene_ontology_edit.obo file
# @arg $3 string go_terms.tab file
# @arg $4 string All_SGD_GOTerms_for_QHTCPtk.csv
# @arg $5 string ZScores_interaction.csv
# @arg $6 string base directory
# @arg $7 string output directory
library("ontologyIndex") library("ontologyIndex")
library("ggplot2") library("ggplot2")
@@ -10,93 +23,43 @@ library("extrafont")
library("stringr") library("stringr")
library("org.Sc.sgd.db") library("org.Sc.sgd.db")
library("ggrepel") library("ggrepel")
library(gplots) library("gplots")
Wstudy=getwd()
inputFile= 'asdf'
inputFile[1] <- "../Exp1/ZScores/ZScores_Interaction.csv" #paste0(Wstudy,"/Exp1/ZScores/ZScores_Interaction.csv")
inputFile[2] <- "../Exp2/ZScores/ZScores_Interaction.csv"
inputFile[3] <- "../Exp3/ZScores/ZScores_Interaction.csv"
inputFile[4] <- "../Exp4/ZScores/ZScores_Interaction.csv"
inputFile[5] <- "../Exp5/ZScores/ZScores_Interaction.csv"
#labels <- read.delim("ExpLabels.txt",skip=0,as.is=T,row.names=1,strip.white=TRUE) # Load arguments
#labels <- read.delim("StudyInfo.csv",skip=0,as.is=T,row.names=1,strip.white=TRUE) args <- commandArgs(TRUE)
labels<- read.csv(file= "StudyInfo.csv",stringsAsFactors = FALSE) study_info_file <- args[1]
lstExpNum= 'asdf' ontology_file <- args[2]
a=0 sgd_terms_tfile <- args[3]
#R can't index data.frame's so some stupid nasty code must be implemented all_sgd_terms_csv <- args[4]
if (file.exists(inputFile[1])){ zscores_file <- args[5]
X1 <- (read.csv(file = inputFile[1],stringsAsFactors=FALSE,header = TRUE)) base_dir <- args[6]
a=a+1 output_dir <- args[7]
lstExpNum[a]= 1 study_nums <- args[8:length(args)]
Name1 <- labels[1,2]} #ssArg2 These are now supplied by Code/ExpLabels.txt which is user edited
if (file.exists(inputFile[2])){
X2 <- (read.csv(file = inputFile[2],stringsAsFactors=FALSE,header = TRUE))
a=a+1
lstExpNum[a]= 2
Name2 <- labels[2,2]}
if (file.exists(inputFile[3])){
X3 <- (read.csv(file = inputFile[3],stringsAsFactors=FALSE,header = TRUE))
a=a+1
lstExpNum[a]= 3
Name3 <- labels[3,2]} #ssArg2 These are now supplied by Code/ExpLabels.txt which is user edited
if (file.exists(inputFile[4])){
X4 <- (read.csv(file = inputFile[4],stringsAsFactors=FALSE,header = TRUE))
a=a+1
lstExpNum[a]= 4
Name4 <- labels[4,2]}
if (file.exists(inputFile[5])){
X5 <- (read.csv(file = inputFile[5],stringsAsFactors=FALSE,header = TRUE))
a=a+1
lstExpNum[a]= 5
Name5 <- labels[5,2]}
#--------------------------Standard Names-------------------------------------------------------
#ExpNames= c('Exp1','Exp2','Exp3','Exp4','Exp5')
#expNumber1<- as.numeric(sub("^.*?(\\d+)$", "\\1", expNm[1]))
#expNumber2<- as.numeric(sub("^.*?(\\d+)$", "\\1", expNm[2]))
#expNumber3<- as.numeric(sub("^.*?(\\d+)$", "\\1", expNm[3]))
#expNumber4<- as.numeric(sub("^.*?(\\d+)$", "\\1", expNm[4]))
#Name1= ExpNames[1]
#Name2= ExpNames[2]
#Name3= ExpNames[3]
#Name4= ExpNames[4]
#Name5= ExpNames[5]
print('52')
#----------------------TABLES------------------------------------------------------------
#import standard tables used in Sean's code That should be copied to each ExpStudy #import standard tables used in Sean's code That should be copied to each ExpStudy
ontology_obo_input <- "gene_ontology_edit.obo" #paste0(Wstudy,"/Code/gene_ontology_edit.obo") # Args[5] labels<- read.csv(file=study_info_file,stringsAsFactors = FALSE)
GOtermstab_file <- "go_terms.tab" Ontology <- get_ontology(file=ontology_file,propagate_relationships = "is_a",extract_tags = "minimal")
GO_ID_Arg <-"All_SGD_GOTerms_for_QHTCPtk.csv" #All_SGD_GOTerms.csv #Args[7]
Ontology <- get_ontology(file=ontology_obo_input,propagate_relationships = "is_a",extract_tags = "minimal")
GO2ALLORFs <- as.list(org.Sc.sgdGO2ALLORFS) #all ORFs associated with GO term GO2ALLORFs <- as.list(org.Sc.sgdGO2ALLORFS) #all ORFs associated with GO term
Terms <- read.delim(file=GOtermstab_file,header=FALSE,quote = "",col.names = c("GO_ID","GO_Term","GO_Aspect","GO_Term_Definition")) Terms <- read.delim(file=sgd_terms_tfile,header=FALSE,quote = "",col.names = c("GO_ID","GO_Term","GO_Aspect","GO_Term_Definition"))
#---------------------------------------------------------------------------- XX3 <- read.csv(file=all_sgd_terms_csv,stringsAsFactors=FALSE,header = TRUE)
#The directory to put the results into. Sean puts this in the 'Home' directory
subDir <- "../TermSpecificHeatmaps"
if (file.exists(subDir)){
outputpath <- subDir
} else {
dir.create(file.path(subDir))
}
outputpath <- "../TermSpecificHeatmaps/" #paste0(Wstudy,"/TermSpecificHeatmaps/")
print(outputpath)
print('73')
#-----------------------------------------------------------------------------------
XX3 <- read.csv(file = GO_ID_Arg,stringsAsFactors=FALSE,header = TRUE)
XX3[,1] <- paste("GO:",formatC(XX3[,1],width=7,flag="0"),sep="") XX3[,1] <- paste("GO:",formatC(XX3[,1],width=7,flag="0"),sep="")
XX3[,2] <- gsub(pattern = " ",replacement = "_",x = XX3[,2]) XX3[,2] <- gsub(pattern = " ",replacement = "_",x = XX3[,2])
XX3[,2] <- gsub(pattern = "/",replacement = "_",x = XX3[,2]) XX3[,2] <- gsub(pattern = "/",replacement = "_",x = XX3[,2])
print('80')
#rm(X,) # Load input files
#Exp1-------------------------------------------------- for (study_num in study_nums) {
if (file.exists(inputFile[1])){ input_file <- file.path(base_dir,paste('Exp',study_num),zscores_file)
print('84') if (file.exists(input_file)) {
assign(paste(X, study_num), read.csv(file=input_file,stringsAsFactors=FALSE,header=TRUE))
assign(paste(Name, study_num), labels[study_num,2])
}
}
for (study_num in study_nums) {
eval(paste("function",study_num))
}
if (length(study_nums) > 0) {
X1$ORF <- X1$OrfRep X1$ORF <- X1$OrfRep
X1$ORF <- gsub("_1","",x=X1$ORF) X1$ORF <- gsub("_1","",x=X1$ORF)
X1$ORF <- gsub("_2","",x=X1$ORF) X1$ORF <- gsub("_2","",x=X1$ORF)
@@ -121,11 +84,9 @@ if (file.exists(inputFile[1])){
X1 <- X1[order(X1$OrfRep,decreasing = FALSE),] X1 <- X1[order(X1$OrfRep,decreasing = FALSE),]
colnames(X1) <- paste(colnames(X1),"_X1",sep="") colnames(X1) <- paste(colnames(X1),"_X1",sep="")
print('110')
} }
print('112')
#Exp2------------------------------------------------------------------------ if (length(study_nums) > 1) {
if (file.exists(inputFile[2])){
X2$ORF <- X2$OrfRep X2$ORF <- X2$OrfRep
X2$ORF <- gsub("_1","",x=X2$ORF) X2$ORF <- gsub("_1","",x=X2$ORF)
X2$ORF <- gsub("_2","",x=X2$ORF) X2$ORF <- gsub("_2","",x=X2$ORF)
@@ -151,11 +112,9 @@ if (file.exists(inputFile[2])){
X2 <- X2[order(X2$OrfRep,decreasing = FALSE),] X2 <- X2[order(X2$OrfRep,decreasing = FALSE),]
colnames(X2) <- paste(colnames(X2),"_X2",sep="") colnames(X2) <- paste(colnames(X2),"_X2",sep="")
X <- cbind(X1,X2) X <- cbind(X1,X2)
print('file2-140')
} }
print('142')
#Exp3-------------------------------------------------------------- if (length(study_nums) > 2) {
if (file.exists(inputFile[3])){
X3$ORF <- X3$OrfRep X3$ORF <- X3$OrfRep
X3$ORF <- gsub("_1","",x=X3$ORF) X3$ORF <- gsub("_1","",x=X3$ORF)
X3$ORF <- gsub("_2","",x=X3$ORF) X3$ORF <- gsub("_2","",x=X3$ORF)
@@ -183,8 +142,7 @@ if (file.exists(inputFile[3])){
X <- cbind(X,X3) X <- cbind(X,X3)
} }
#Exp4 if (length(study_nums) > 3) {
if (file.exists(inputFile[4])){
X4$ORF <- X4$OrfRep X4$ORF <- X4$OrfRep
X4$ORF <- gsub("_1","",x=X4$ORF) X4$ORF <- gsub("_1","",x=X4$ORF)
X4$ORF <- gsub("_2","",x=X4$ORF) X4$ORF <- gsub("_2","",x=X4$ORF)
@@ -212,8 +170,7 @@ if (file.exists(inputFile[4])){
X <- cbind(X,X4) X <- cbind(X,X4)
} }
#Exp5-------------------------------------------------------------- if (length(study_nums) > 4) {
if (file.exists(inputFile[5])){
X5$ORF <- X5$OrfRep X5$ORF <- X5$OrfRep
X5$ORF <- gsub("_1","",x=X5$ORF) X5$ORF <- gsub("_1","",x=X5$ORF)
X5$ORF <- gsub("_2","",x=X5$ORF) X5$ORF <- gsub("_2","",x=X5$ORF)
@@ -240,12 +197,11 @@ if (file.exists(inputFile[5])){
colnames(X5) <- paste(colnames(X5),"_X5",sep="") colnames(X5) <- paste(colnames(X5),"_X5",sep="")
X <- cbind(X,X5) X <- cbind(X,X5)
} }
print('after5-229')
X$ORF <- X$OrfRep_X1
part1=1
if (file.exists(inputFile[1])& file.exists(inputFile[2])){ X$ORF <- X$OrfRep_X1
print('234 ifFile2')
if (length(study_nums) > 1) {
X$ORF <- gsub("_1","",x=X$ORF) X$ORF <- gsub("_1","",x=X$ORF)
try(X[X$Gene_X1 == "",]$Gene_X1 <- X[X$Gene_X1 == "",]$OrfRep_X1) try(X[X$Gene_X1 == "",]$Gene_X1 <- X[X$Gene_X1 == "",]$OrfRep_X1)
@@ -263,7 +219,7 @@ if (file.exists(inputFile[1])& file.exists(inputFile[2])){
} }
if (file.exists(inputFile[3])){ if (length(study_nums) > 2) {
X$ORF <- gsub("_1","",x=X$ORF) X$ORF <- gsub("_1","",x=X$ORF)
X$ORF <- gsub("_2","",x=X$ORF) X$ORF <- gsub("_2","",x=X$ORF)
@@ -286,7 +242,7 @@ if (file.exists(inputFile[3])){
colnames(X_heatmap)[2] <- "Gene" colnames(X_heatmap)[2] <- "Gene"
} }
if (file.exists(inputFile[4])){ if (length(study_nums) > 3) {
X$ORF <- gsub("_1","",x=X$ORF) X$ORF <- gsub("_1","",x=X$ORF)
X$ORF <- gsub("_2","",x=X$ORF) X$ORF <- gsub("_2","",x=X$ORF)
X$ORF <- gsub("_3","",x=X$ORF) X$ORF <- gsub("_3","",x=X$ORF)
@@ -315,7 +271,7 @@ if (file.exists(inputFile[4])){
} }
if (file.exists(inputFile[5])){ if (length(study_nums) > 4) {
X$ORF <- gsub("_1","",x=X$ORF) X$ORF <- gsub("_1","",x=X$ORF)
X$ORF <- gsub("_2","",x=X$ORF) X$ORF <- gsub("_2","",x=X$ORF)
X$ORF <- gsub("_3","",x=X$ORF) X$ORF <- gsub("_3","",x=X$ORF)
@@ -350,8 +306,6 @@ if (file.exists(inputFile[5])){
} }
#-----------------------------------------------------------------------------------------
#theme elements for plots #theme elements for plots
theme_Publication <- function(base_size=14, base_family="sans") { theme_Publication <- function(base_size=14, base_family="sans") {
(theme_foundation(base_size=base_size, base_family=base_family) (theme_foundation(base_size=base_size, base_family=base_family)
@@ -434,27 +388,15 @@ scale_colour_Publication <- function(...){
} }
Ontology <- get_ontology(file=ontology_file,propagate_relationships = "is_a",extract_tags = "minimal")
#www.geneontology.org/ontology/gene_ontology_edit.obo file
Ontology <- get_ontology(file=ontology_obo_input,propagate_relationships = "is_a",extract_tags = "minimal")
print(Ontology) print(Ontology)
#all ORFs associated with GO term #all ORFs associated with GO term
GO2ALLORFs <- as.list(org.Sc.sgdGO2ALLORFS) GO2ALLORFs <- as.list(org.Sc.sgdGO2ALLORFS)
print('429')
#Gene_Association is the gene association to GO term file
#Gene_Association <- read.delim("Documents/Hartman_Lab/SGD_Downloads/gene_association.sgd",skip=8,header=FALSE,quote="",col.names = c("Database","Database_Object_ID","Database_Object_Symbol","NOT","GO_ID","Database_Reference","Evidence","With_or_From","Aspect","Database_Object_Name","Database_Object_Synonym","Database_Object_Type","taxon","Date","Assigned_By","OtherInfo","Empty"))
#Gene_Association$ORF <- str_split_fixed(as.character(Gene_Association$Database_Object_Synonym),"\\|",2)[,1]
#Gene_Association$GO_ID_Numeric <- as.integer(str_split_fixed(as.character(Gene_Association$GO_ID),"\\:",2)[,2])
#Terms is the GO term list jwr moved up to TAABLES #Terms is the GO term list jwr moved up to TAABLES
Terms <- read.delim(file=GOtermstab_file,header=FALSE,quote = "",col.names = c("GO_ID","GO_Term","GO_Aspect","GO_Term_Definition")) Terms <- read.delim(file=sgd_terms_tfile,header=FALSE,quote = "",col.names = c("GO_ID","GO_Term","GO_Aspect","GO_Term_Definition"))
#-----------------------------------------------------------------------
#-----------------------------------------------------------------------------------------------------
#BIG LOOP BIG LOOP ------------------------------------------------------ #BIG LOOP BIG LOOP ------------------------------------------------------
colormapbreaks <- c(-12,-10,-8,-6,-4,-2,2,4,6,8,10,12) colormapbreaks <- c(-12,-10,-8,-6,-4,-2,2,4,6,8,10,12)
for(s in 1:dim(XX3)[1]){ for(s in 1:dim(XX3)[1]){
@@ -466,23 +408,18 @@ for(s in 1:dim(XX3)[1]){
#GOTerm_parent <- get_descendants(Ontology,roots = "GO:0006325") #GOTerm_parent <- get_descendants(Ontology,roots = "GO:0006325")
#only make plots if parent term has fewer than 500 children #only make plots if parent term has fewer than 500 children
print('for(s in 1:dim(XX3)[1]){ -454') Parent_Size <- length(as.vector(GO2ALLORFs[GO_ID_Arg_loop][[1]]))
Parent_Size <- length(as.vector(GO2ALLORFs[GO_ID_Arg_loop][[1]]))
if(length(GOTerm_parent) > 100){ if(length(GOTerm_parent) > 100){
#print(length(GOTerm_parent))
next() next()
} }
Parent_Size <- length(as.vector(GO2ALLORFs[GO_ID_Arg_loop][[1]])) Parent_Size <- length(as.vector(GO2ALLORFs[GO_ID_Arg_loop][[1]]))
if(Parent_Size < 2){ if(Parent_Size < 2){
next() next()
} }
if(Parent_Size > 2000){ if(Parent_Size > 2000){
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 45, onefile = TRUE) pdf(file=paste(output_dir,XX3[s,2],".pdf",sep=""),width = 12, height = 45, onefile = TRUE)
print('pdf2000 469')
for(i in 1:length(GOTerm_parent)){ for(i in 1:length(GOTerm_parent)){
GO_Term <- GOTerm_parent[i] GO_Term <- GOTerm_parent[i]
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2]) GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
@@ -509,7 +446,7 @@ for(s in 1:dim(XX3)[1]){
} }
if(Parent_Size >= 1000 && Parent_Size <= 2000){ if(Parent_Size >= 1000 && Parent_Size <= 2000){
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 35, onefile = TRUE) pdf(file=paste(output_dir,XX3[s,2],".pdf",sep=""),width = 12, height = 35, onefile = TRUE)
for(i in 1:length(GOTerm_parent)){ for(i in 1:length(GOTerm_parent)){
GO_Term <- GOTerm_parent[i] GO_Term <- GOTerm_parent[i]
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2]) GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
@@ -535,7 +472,7 @@ for(s in 1:dim(XX3)[1]){
dev.off() dev.off()
} }
if(Parent_Size >= 500 && Parent_Size <= 1000){ if(Parent_Size >= 500 && Parent_Size <= 1000){
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 30, onefile = TRUE) pdf(file=paste(output_dir,XX3[s,2],".pdf",sep=""),width = 12, height = 30, onefile = TRUE)
for(i in 1:length(GOTerm_parent)){ for(i in 1:length(GOTerm_parent)){
GO_Term <- GOTerm_parent[i] GO_Term <- GOTerm_parent[i]
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2]) GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
@@ -561,7 +498,7 @@ for(s in 1:dim(XX3)[1]){
dev.off() dev.off()
} }
if(Parent_Size >= 200 && Parent_Size <= 500){ if(Parent_Size >= 200 && Parent_Size <= 500){
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 25, onefile = TRUE) pdf(file=paste(output_dir,XX3[s,2],".pdf",sep=""),width = 12, height = 25, onefile = TRUE)
for(i in 1:length(GOTerm_parent)){ for(i in 1:length(GOTerm_parent)){
GO_Term <- GOTerm_parent[i] GO_Term <- GOTerm_parent[i]
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2]) GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
@@ -587,7 +524,7 @@ for(s in 1:dim(XX3)[1]){
dev.off() dev.off()
} }
if(Parent_Size >= 100 && Parent_Size <= 200){ if(Parent_Size >= 100 && Parent_Size <= 200){
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 20, onefile = TRUE) pdf(file=paste(output_dir,XX3[s,2],".pdf",sep=""),width = 12, height = 20, onefile = TRUE)
for(i in 1:length(GOTerm_parent)){ for(i in 1:length(GOTerm_parent)){
GO_Term <- GOTerm_parent[i] GO_Term <- GOTerm_parent[i]
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2]) GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
@@ -613,7 +550,7 @@ for(s in 1:dim(XX3)[1]){
dev.off() dev.off()
} }
if(Parent_Size >= 60 && Parent_Size <= 100){ if(Parent_Size >= 60 && Parent_Size <= 100){
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 15, onefile = TRUE) pdf(file=paste(output_dir,XX3[s,2],".pdf",sep=""),width = 12, height = 15, onefile = TRUE)
for(i in 1:length(GOTerm_parent)){ for(i in 1:length(GOTerm_parent)){
GO_Term <- GOTerm_parent[i] GO_Term <- GOTerm_parent[i]
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2]) GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
@@ -639,7 +576,7 @@ for(s in 1:dim(XX3)[1]){
dev.off() dev.off()
} }
if(Parent_Size >= 30 && Parent_Size <= 60){ if(Parent_Size >= 30 && Parent_Size <= 60){
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 10, onefile = TRUE) pdf(file=paste(output_dir,XX3[s,2],".pdf",sep=""),width = 12, height = 10, onefile = TRUE)
for(i in 1:length(GOTerm_parent)){ for(i in 1:length(GOTerm_parent)){
GO_Term <- GOTerm_parent[i] GO_Term <- GOTerm_parent[i]
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2]) GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
@@ -679,7 +616,7 @@ for(s in 1:dim(XX3)[1]){
dev.off() dev.off()
} }
if(Parent_Size >= 3 && Parent_Size <= 30){ if(Parent_Size >= 3 && Parent_Size <= 30){
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 7, onefile = TRUE) pdf(file=paste(output_dir,XX3[s,2],".pdf",sep=""),width = 12, height = 7, onefile = TRUE)
for(i in 1:length(GOTerm_parent)){ for(i in 1:length(GOTerm_parent)){
GO_Term <- GOTerm_parent[i] GO_Term <- GOTerm_parent[i]
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2]) GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
@@ -718,7 +655,7 @@ for(s in 1:dim(XX3)[1]){
dev.off() dev.off()
} }
if(Parent_Size == 2){ if(Parent_Size == 2){
pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 7, onefile = TRUE) pdf(file=paste(output_dir,XX3[s,2],".pdf",sep=""),width = 12, height = 7, onefile = TRUE)
for(i in 1:length(GOTerm_parent)){ for(i in 1:length(GOTerm_parent)){
GO_Term <- GOTerm_parent[i] GO_Term <- GOTerm_parent[i]
GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2]) GO_Term_Num <- as.integer(str_split_fixed(as.character(GO_Term),"\\:",2)[,2])
@@ -753,13 +690,7 @@ for(s in 1:dim(XX3)[1]){
#ColSideColors=ev_repeat, #ColSideColors=ev_repeat,
labRow=as.character(Genes_Annotated_to_Term$Gene))) labRow=as.character(Genes_Annotated_to_Term$Gene)))
} }
print('740')
} }
dev.off() dev.off()
} }
} }

14
workflow/templates/qhtcp/ExpTemplate/Notes Normal file
View File

@@ -0,0 +1,14 @@
// Copyright 2024 Bryan C. Roessler
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// https://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.

0
workflow/templates/qhtcp/ExpTemplate/NotesExp1
View File

4
workflow/templates/qhtcp/ExpTemplate/Z_InteractionTemplate.R
View File

@@ -1,4 +1,4 @@
#!/usr/bin/env R #!/usr/bin/env Rscript
# Based on InteractionTemplate.R which is based on Sean Santos's Interaction_V5 script # Based on InteractionTemplate.R which is based on Sean Santos's Interaction_V5 script
# #
# Updated 240724 Bryan C Roessler to improve file operations and portability # Updated 240724 Bryan C Roessler to improve file operations and portability
@@ -23,8 +23,6 @@ library("htmlwidgets")
# Parse arguments # Parse arguments
args <- commandArgs(TRUE) args <- commandArgs(TRUE)
# Set input file (required)
inputFile <- args[1] inputFile <- args[1]
# Set output dir # Set output dir