diff --git a/workflow/script-run-workflow b/workflow/script-run-workflow index f1f92c65..c372fdd5 100755 --- a/workflow/script-run-workflow +++ b/workflow/script-run-workflow @@ -5,8 +5,7 @@ # Allow indirect functions # shellcheck disable=SC2317 # -# shdoc info -# @name HartmanLabWorkflow +# @name Hartman Lab Self-Documenting Workflow # @brief One script to rule them all (see: xkcd #927) # @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): @@ -27,7 +26,6 @@ DEBUG=1 # Turn debugging ON by default during development shopt -s extglob - # @section Libraries # @description Change these variables to use different libraries JAVA="${JAVA:-java}" @@ -59,7 +57,7 @@ print_help() { --exclude, -x MODULE See MODULES section below for list of modules to exclude --markdown, -m - Generate the shdoc markdown file for this program + Generate the shdoc markdown README.md file for this program --yes, -y, --auto Always answer yes to questions (non-interactive mode) --debug, -d @@ -135,7 +133,7 @@ parse_input() { fi ;; --markdown|-m) - documentation + documentation; exit 0 # TODO disable the exit after development ;; --yes|-y|--auto) 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. # 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. # 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 # Run remc as part of the QHTCP process - remc } @@ -1043,29 +743,88 @@ gtf() { module gta # @section GTA # @description GTA module for QHTCP -# TODO +# NOTES # * 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() { 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_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 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 - zscores_file="$QHTCP_PROJECT_DIR/Exp$s/ZScores/ZScores_Interaction.csv" + zscores_file="$QHTCP_PROJECT_DIR/Exp$s/$zscores_file" if [[ -f $zscores_file ]]; then - mkdir "$gta_out_dir/Exp$s" - r_gta "Exp$s" "$zscores_file" "$sgd_terms_tfile" "$sgd_features_file" "$gta_out_dir" + mkdir "$GTA_OUT_DIR/Exp$s" + r_gta "Exp$s" "$zscores_file" "$sgd_terms_tfile" "$sgd_features_file" "$GTA_OUT_DIR" fi done + + # Combination studies (for pairwise comparisons) + for combo in "${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" + [[ -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 $*" "$RSCRIPT" "$script" "$@" } @@ -1452,7 +1293,7 @@ documentation() { # Print markdown to stdout ((DEBUG)) && shdoc < "$SCRIPT" # Create markdown file - shdoc < "$SCRIPT" > documentation.md + shdoc < "$SCRIPT" > README.md } @@ -1460,6 +1301,7 @@ documentation() { # May eventually need to add git ops # Passes on arguments # Most variables in main() are user configurable or can be overriden by env +# @internal main() { debug "Running: ${FUNCNAME[0]}" "$@" @@ -1547,3 +1389,305 @@ main() { main "$@" 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) \ No newline at end of file diff --git a/workflow/templates/qhtcp/Code/PairwiseLK.R b/workflow/templates/qhtcp/Code/PairwiseLK.R index 83042cf2..5e2c3eac 100644 --- a/workflow/templates/qhtcp/Code/PairwiseLK.R +++ b/workflow/templates/qhtcp/Code/PairwiseLK.R @@ -1,41 +1,67 @@ -#4.This R script performs GTA L and K Pairwise Compares for user specified pairs of Experiments -#Arg1 is the first Experiment or a user ordered pair (i.e., Exp3) -#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 -#which correlates the canonical Exp Name with the user stylized label for plots and output files. +#!/usr/bin/env Rscript +# This R script performs GTA L and K Pairwise Compares for user specified pairs of Experiments +# +# Updated 240724 Bryan C Roessler to improve file operations and portability +# 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) -library(plotly) -library(htmlwidgets) -library(extrafont) -library(grid) -library(ggthemes) -Args <- commandArgs(TRUE) +args <- commandArgs(TRUE) +exp_name <- args[1] +exp_name2 <- args[2] -expNm= Args[1] #i.e., "Exp3" -expNm[2]= Args[2] #i.e., "Exp4" -expNumber1<- as.numeric(sub("^.*?(\\d+)$", "\\1", expNm[1])) -expNumber2<- as.numeric(sub("^.*?(\\d+)$", "\\1", expNm[2])) -#labels <- read.delim("ExpLabels.txt",skip=0,as.is=T,row.names=1,strip.white=TRUE) -#labels <- read.delim("StudyInfo.csv",skip=0,as.is=T,row.names=1,strip.white=TRUE) -Labels<- read.csv(file= "StudyInfo.csv",stringsAsFactors = FALSE) -Name1 <- Labels[expNumber1,2] #ssArg2 These are now supplied by Code/ExpLabels.csv which is user edited -Name2 <- Labels[expNumber2,2] #ssArg4 -Wstudy= getwd() -input_file1 <- paste0("../GTAresults/",expNm[1],"/Average_GOTerms_All.csv" ) #Args[1] -input_file2 <- paste0("../GTAresults/",expNm[2],"/Average_GOTerms_All.csv" ) #Args[3] +if (length(args) > 3) { + study_info_file <- args[3] +} else { + study_info_file <- "StudyInfo.csv" +} -pairDirL= paste0("../GTAresults/","PairwiseCompareL_",expNm[1],"-",expNm[2]) -pairDirK= paste0("../GTAresults/","PairwiseCompareK_",expNm[1],"-",expNm[2]) -outPathGTAcompare= "../GTAresults/PairwiseCompareL" #paste0(Wstudy,"/GTAresults/PairwiseCompareL) -outPathGTAcompare[2]= "../GTAresults/PairwiseCompareK" #paste0(Wstudy,"/GTAresults/PairwiseCompareK") +if (length(args) > 4) { + output_dir <- args[4] +} else { + output_dir <- "../GTAresults" +} + +# if (length(args) > 3) { +# sgd_terms_file <- args[3] +# } else { +# sgd_terms_file <- "../Code/go_terms.tab" +# } + +# if (length(args) > 4) { +# sgd_features_file <- args[4] +# } else { +# sgd_features_file <- "../Code/gene_association.sgd" +# } + +expNumber1<- as.numeric(sub("^.*?(\\d+)$", "\\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(pairDirL) #(outPathGTAcompare[1]) dir.create(pairDirK) #(outPathGTAcompare[2]) ###########BEGIN PAIRWISE L-----LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL -#define the output path (as fourth argument from Rscript) outputpath <- pairDirL #outPathGTAcompare[1] #Args[5] #outputPlotly <- "../GTAresults/PairwiseCompareL/" #"/GTAresults/PairwiseCompareL/" print("39") diff --git a/workflow/templates/qhtcp/Code/TSHeatmaps5dev2.R b/workflow/templates/qhtcp/Code/TSHeatmaps5dev2.R index bdbe80bd..e7478540 100644 --- a/workflow/templates/qhtcp/Code/TSHeatmaps5dev2.R +++ b/workflow/templates/qhtcp/Code/TSHeatmaps5dev2.R @@ -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("ggplot2") @@ -10,93 +23,43 @@ library("extrafont") library("stringr") library("org.Sc.sgd.db") library("ggrepel") -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" +library("gplots") + +# Load arguments +args <- commandArgs(TRUE) +study_info_file <- args[1] +ontology_file <- args[2] +sgd_terms_tfile <- args[3] +all_sgd_terms_csv <- args[4] +zscores_file <- args[5] +base_dir <- args[6] +output_dir <- args[7] +study_nums <- args[8:length(args)] -#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) -lstExpNum= 'asdf' -a=0 -#R can't index data.frame's so some stupid nasty code must be implemented -if (file.exists(inputFile[1])){ - X1 <- (read.csv(file = inputFile[1],stringsAsFactors=FALSE,header = TRUE)) - a=a+1 - lstExpNum[a]= 1 - 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 -ontology_obo_input <- "gene_ontology_edit.obo" #paste0(Wstudy,"/Code/gene_ontology_edit.obo") # Args[5] -GOtermstab_file <- "go_terms.tab" -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") +labels<- read.csv(file=study_info_file,stringsAsFactors = FALSE) +Ontology <- get_ontology(file=ontology_file,propagate_relationships = "is_a",extract_tags = "minimal") 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")) -#---------------------------------------------------------------------------- - -#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) - +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) 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]) -print('80') -#rm(X,) -#Exp1-------------------------------------------------- -if (file.exists(inputFile[1])){ - print('84') + +# Load input files +for (study_num in study_nums) { + input_file <- file.path(base_dir,paste('Exp',study_num),zscores_file) + 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 <- gsub("_1","",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),] colnames(X1) <- paste(colnames(X1),"_X1",sep="") - print('110') } -print('112') -#Exp2------------------------------------------------------------------------ -if (file.exists(inputFile[2])){ + +if (length(study_nums) > 1) { X2$ORF <- X2$OrfRep X2$ORF <- gsub("_1","",x=X2$ORF) X2$ORF <- gsub("_2","",x=X2$ORF) @@ -151,11 +112,9 @@ if (file.exists(inputFile[2])){ X2 <- X2[order(X2$OrfRep,decreasing = FALSE),] colnames(X2) <- paste(colnames(X2),"_X2",sep="") X <- cbind(X1,X2) - print('file2-140') } -print('142') -#Exp3-------------------------------------------------------------- -if (file.exists(inputFile[3])){ + +if (length(study_nums) > 2) { X3$ORF <- X3$OrfRep X3$ORF <- gsub("_1","",x=X3$ORF) X3$ORF <- gsub("_2","",x=X3$ORF) @@ -183,8 +142,7 @@ if (file.exists(inputFile[3])){ X <- cbind(X,X3) } -#Exp4 -if (file.exists(inputFile[4])){ +if (length(study_nums) > 3) { X4$ORF <- X4$OrfRep X4$ORF <- gsub("_1","",x=X4$ORF) X4$ORF <- gsub("_2","",x=X4$ORF) @@ -212,8 +170,7 @@ if (file.exists(inputFile[4])){ X <- cbind(X,X4) } -#Exp5-------------------------------------------------------------- -if (file.exists(inputFile[5])){ +if (length(study_nums) > 4) { X5$ORF <- X5$OrfRep X5$ORF <- gsub("_1","",x=X5$ORF) X5$ORF <- gsub("_2","",x=X5$ORF) @@ -240,12 +197,11 @@ if (file.exists(inputFile[5])){ colnames(X5) <- paste(colnames(X5),"_X5",sep="") X <- cbind(X,X5) } -print('after5-229') -X$ORF <- X$OrfRep_X1 -part1=1 -if (file.exists(inputFile[1])& file.exists(inputFile[2])){ - print('234 ifFile2') +X$ORF <- X$OrfRep_X1 + +if (length(study_nums) > 1) { + X$ORF <- gsub("_1","",x=X$ORF) try(X[X$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("_2","",x=X$ORF) @@ -286,7 +242,7 @@ if (file.exists(inputFile[3])){ colnames(X_heatmap)[2] <- "Gene" } -if (file.exists(inputFile[4])){ +if (length(study_nums) > 3) { X$ORF <- gsub("_1","",x=X$ORF) X$ORF <- gsub("_2","",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("_2","",x=X$ORF) X$ORF <- gsub("_3","",x=X$ORF) @@ -350,8 +306,6 @@ if (file.exists(inputFile[5])){ } -#----------------------------------------------------------------------------------------- - #theme elements for plots theme_Publication <- function(base_size=14, base_family="sans") { (theme_foundation(base_size=base_size, base_family=base_family) @@ -434,27 +388,15 @@ scale_colour_Publication <- function(...){ } - -#www.geneontology.org/ontology/gene_ontology_edit.obo file -Ontology <- get_ontology(file=ontology_obo_input,propagate_relationships = "is_a",extract_tags = "minimal") +Ontology <- get_ontology(file=ontology_file,propagate_relationships = "is_a",extract_tags = "minimal") print(Ontology) #all ORFs associated with GO term GO2ALLORFs <- as.list(org.Sc.sgdGO2ALLORFS) -print('429') - - -#Gene_Association is the gene association to GO term file -#Gene_Association <- read.delim("Documents/Hartman_Lab/SGD_Downloads/gene_association.sgd",skip=8,header=FALSE,quote="",col.names = c("Database","Database_Object_ID","Database_Object_Symbol","NOT","GO_ID","Database_Reference","Evidence","With_or_From","Aspect","Database_Object_Name","Database_Object_Synonym","Database_Object_Type","taxon","Date","Assigned_By","OtherInfo","Empty")) -#Gene_Association$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 <- 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 ------------------------------------------------------ colormapbreaks <- c(-12,-10,-8,-6,-4,-2,2,4,6,8,10,12) for(s in 1:dim(XX3)[1]){ @@ -465,24 +407,19 @@ for(s in 1:dim(XX3)[1]){ GOTerm_parent <- get_descendants(Ontology,roots = GO_ID_Arg_loop) #GOTerm_parent <- get_descendants(Ontology,roots = "GO:0006325") #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){ - #print(length(GOTerm_parent)) next() } - Parent_Size <- length(as.vector(GO2ALLORFs[GO_ID_Arg_loop][[1]])) if(Parent_Size < 2){ next() } if(Parent_Size > 2000){ - pdf(file=paste(outputpath,XX3[s,2],".pdf",sep=""),width = 12, height = 45, onefile = TRUE) - print('pdf2000 469') + pdf(file=paste(output_dir,XX3[s,2],".pdf",sep=""),width = 12, height = 45, onefile = TRUE) for(i in 1:length(GOTerm_parent)){ GO_Term <- GOTerm_parent[i] 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){ - 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)){ GO_Term <- GOTerm_parent[i] 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() } 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)){ GO_Term <- GOTerm_parent[i] 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() } 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)){ GO_Term <- GOTerm_parent[i] 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() } 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)){ GO_Term <- GOTerm_parent[i] 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() } 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)){ GO_Term <- GOTerm_parent[i] 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() } 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)){ GO_Term <- GOTerm_parent[i] 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() } 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)){ GO_Term <- GOTerm_parent[i] 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() } 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)){ GO_Term <- GOTerm_parent[i] 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, labRow=as.character(Genes_Annotated_to_Term$Gene))) } - print('740') } dev.off() } - - - - } - diff --git a/workflow/templates/qhtcp/ExpTemplate/Notes b/workflow/templates/qhtcp/ExpTemplate/Notes new file mode 100644 index 00000000..1f671bc1 --- /dev/null +++ b/workflow/templates/qhtcp/ExpTemplate/Notes @@ -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. + diff --git a/workflow/templates/qhtcp/ExpTemplate/NotesExp1 b/workflow/templates/qhtcp/ExpTemplate/NotesExp1 deleted file mode 100644 index e69de29b..00000000 diff --git a/workflow/templates/qhtcp/ExpTemplate/Z_InteractionTemplate.R b/workflow/templates/qhtcp/ExpTemplate/Z_InteractionTemplate.R index 679dc745..e91a4019 100644 --- a/workflow/templates/qhtcp/ExpTemplate/Z_InteractionTemplate.R +++ b/workflow/templates/qhtcp/ExpTemplate/Z_InteractionTemplate.R @@ -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 # # Updated 240724 Bryan C Roessler to improve file operations and portability @@ -23,8 +23,6 @@ library("htmlwidgets") # Parse arguments args <- commandArgs(TRUE) - -# Set input file (required) inputFile <- args[1] # Set output dir