Small bug fixes

swvanderlaan · swvanderlaan · commit 64ae9ef10ec3 · 2018-01-24T21:20:04.000+01:00
Some R-specific lines were 'broken' after the HPC module load update.
Some references to files were broken.
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,3 @@
 RESOURCES
 ~$20161102_AEGS_available_phenotypes_covariates.xlsx
+.DS_Store
diff --git a/SCRIPTS/plotter.effectsize.R b/SCRIPTS/plotter.effectsize.R
@@ -1,4 +1,4 @@
-#!/hpc/local/CentOS7/dhl_ec/software/R-3.4.0/bin/Rscript --vanilla
+#!/usr/local/bin/Rscript --vanilla
 
 ### Mac OS X version
 ### #!/usr/local/bin/Rscript --vanilla
@@ -9,8 +9,8 @@
 cat("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
     Effect Size Plotter -- GWASToolKit
     \n
-    * Version: v1.3.5
-    * Last edit: 2017-08-22
+    * Version: v1.3.6
+    * Last edit: 2018-01-24
     * Created by: Sander W. van der Laan | s.w.vanderlaan@gmail.com
     \n
     * Description:  EffectSize-plotter for GWAS (meta-analysis) results. Can produce output 
diff --git a/SCRIPTS/plotter.infoscore.R b/SCRIPTS/plotter.infoscore.R
@@ -1,4 +1,4 @@
-#!/hpc/local/CentOS7/dhl_ec/software/R-3.4.0/bin/Rscript --vanilla
+#!/usr/local/bin/Rscript --vanilla
 
 ### Mac OS X version
 ### #!/usr/local/bin/Rscript --vanilla
@@ -9,8 +9,8 @@
 cat("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
     Imputation Quality Score Plotter -- GWASToolKit
     \n
-    * Version: v1.4.3
-    * Last edit: 2017-08-22
+    * Version: v1.4.4
+    * Last edit: 2018-01-24
     * Created by: Sander W. van der Laan | s.w.vanderlaan@gmail.com
     \n
     * Description:  INFO-plotter for GWAS (meta-analysis) results. Can produce output 
diff --git a/SCRIPTS/plotter.manhattan.R b/SCRIPTS/plotter.manhattan.R
@@ -1,4 +1,4 @@
-#!/hpc/local/CentOS7/dhl_ec/software/R-3.4.0/bin/Rscript --vanilla
+#!/usr/local/bin/Rscript --vanilla
 
 ### Mac OS X version
 ### #!/usr/local/bin/Rscript --vanilla
@@ -9,8 +9,8 @@
 cat("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
     Manhattan Plotter -- GWASToolKit
     \n
-    * Version: v1.1.6
-    * Last edit: 2017-08-22
+    * Version: v1.1.7
+    * Last edit: 2018-01-24
     * Created by: Sander W. van der Laan | s.w.vanderlaan@gmail.com
     \n
     * Description:  Manhattan-plotter for GWAS (meta-analysis) results. Can produce output 
diff --git a/SCRIPTS/plotter.p_z.R b/SCRIPTS/plotter.p_z.R
@@ -1,4 +1,4 @@
-#!/hpc/local/CentOS7/dhl_ec/software/R-3.4.0/bin/Rscript --vanilla
+#!/usr/local/bin/Rscript --vanilla
 
 ### Mac OS X version
 ### #!/usr/local/bin/Rscript --vanilla
@@ -9,8 +9,8 @@
 cat("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
     P-Z Plotter -- GWASToolKit
     \n
-    * Version: v1.1.5
-    * Last edit: 2017-08-22
+    * Version: v1.1.6
+    * Last edit: 2018-01-24
     * Created by: Sander W. van der Laan | s.w.vanderlaan@gmail.com
     \n
     * Description:  P-Z-plotter for GWAS (meta-analysis) results. Will plot the
diff --git a/SCRIPTS/plotter.qq.R b/SCRIPTS/plotter.qq.R
@@ -1,4 +1,4 @@
-#!/hpc/local/CentOS7/dhl_ec/software/R-3.4.0/bin/Rscript --vanilla
+#!/usr/local/bin/Rscript --vanilla
 
 ### Mac OS X version
 ### #!/usr/local/bin/Rscript --vanilla
@@ -9,8 +9,8 @@
 cat("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
     QQ Plotter -- GWASToolKit
     \n
-    * Version: v1.2.5
-    * Last edit: 2017-08-22
+    * Version: v1.2.6
+    * Last edit: 2018-01-24
     * Created by: Sander W. van der Laan | s.w.vanderlaan@gmail.com
     \n
     * Description:  QQ-Plotter for GWAS (meta-analysis) results. Can produce 
diff --git a/SCRIPTS/plotter.qq_by_caf.R b/SCRIPTS/plotter.qq_by_caf.R
@@ -1,4 +1,4 @@
-#!/hpc/local/CentOS7/dhl_ec/software/R-3.4.0/bin/Rscript --vanilla
+#!/usr/local/bin/Rscript --vanilla
 
 ### Mac OS X version
 ### #!/usr/local/bin/Rscript --vanilla
@@ -9,8 +9,8 @@
 cat("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
     QQ by CAF Plotter -- GWASToolKit
     \n
-    * Version: v1.1.6
-    * Last edit: 2017-08-22
+    * Version: v1.1.7
+    * Last edit: 2018-01-24
     * Created by: Sander W. van der Laan | s.w.vanderlaan@gmail.com
     \n
     * Description: QQ-Plotter for GWAS (meta-analysis) results stratified 
diff --git a/SCRIPTS/plotter.qq_by_info.R b/SCRIPTS/plotter.qq_by_info.R
@@ -1,4 +1,4 @@
-#!/hpc/local/CentOS7/dhl_ec/software/R-3.4.0/bin/Rscript --vanilla
+#!/usr/local/bin/Rscript --vanilla
 
 ### Mac OS X version
 ### #!/usr/local/bin/Rscript --vanilla
@@ -9,8 +9,8 @@
 cat("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
     QQ by INFO-score Plotter -- GWASToolKit
     \n
-    * Version: v1.1.6
-    * Last edit: 2017-08-22
+    * Version: v1.1.7
+    * Last edit: 2018-01-24
     * Created by: Sander W. van der Laan | s.w.vanderlaan@gmail.com
     \n
     * Description: QQ-Plotter for GWAS (meta-analysis) results stratified 
diff --git a/SCRIPTS/plotter.qq_by_type.R b/SCRIPTS/plotter.qq_by_type.R
@@ -1,4 +1,4 @@
-#!/hpc/local/CentOS7/dhl_ec/software/R-3.4.0/bin/Rscript --vanilla
+#!/usr/local/bin/Rscript --vanilla
 
 ### Mac OS X version
 ### #!/usr/local/bin/Rscript --vanilla
@@ -9,8 +9,8 @@
 cat("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
     QQ by TYPE Plotter -- GWASToolKit
     \n
-    * Version: v1.1.6
-    * Last edit: 2017-08-22
+    * Version: v1.1.7
+    * Last edit: 2018-01-24
     * Created by: Sander W. van der Laan | s.w.vanderlaan@gmail.com
     \n
     * Description: QQ-Plotter for GWAS (meta-analysis) results stratified 
diff --git a/SUPPORT/20180122_AEGS_available_phenotypes_covariates.xlsx b/SUPPORT/20180122_AEGS_available_phenotypes_covariates.xlsx
diff --git a/gwastoolkit.locuszoomer.sh b/gwastoolkit.locuszoomer.sh
@@ -96,9 +96,9 @@ echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 echo "                                           GWASTOOLKIT LOCUSZOOMER"
 echo "                                regional association plotting of clumped results"
 echo ""
-echo " Version    : v1.5.0"
+echo " Version    : v1.5.1"
 echo ""
-echo " Last update: 2017-07-07"
+echo " Last update: 2018-01-24"
 echo " Written by : Sander W. van der Laan (s.w.vanderlaan-2@umcutrecht.nl)."
 echo ""
 echo " Description: Plot a LocusZoom for (imputed) (meta-)ExomeChip or (meta-)GWAS hits "
@@ -203,7 +203,7 @@ echo "                                             MAKE LOCUSZOOM PLOTS"
 	if [[ ${ANALYSIS_TYPE} = "GWAS" ]]; then
 		### Which variant to look at.
 		echo "We will lookup the following variants:"
-		VARIANTLIST="${INPUTDIR}/${PHENOTYPE}.summary_results.QC.${CLUMP_R2}.indexvariants.txt" 
+		VARIANTLIST="${INPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.summary_results.QC.${CLUMP_R2}.indexvariants.txt" 
 		while read VARIANTS; do 
 			for VARIANT in ${VARIANTS}; do
 			echo "* ${VARIANT}"
@@ -236,6 +236,10 @@ echo "                                             MAKE LOCUSZOOM PLOTS"
 			
 			done
 		done < ${VARIANTLIST}
+		
+		# gzipping locuszoom input
+		gzip -v ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom 
+		
 		echo ""
 		echo "All finished. Done making regional association plots for ${PHENOTYPE} data."
 		echo ""
@@ -274,6 +278,9 @@ echo "                                             MAKE LOCUSZOOM PLOTS"
 
 		done < ${REGIONS_FILE}		
 		
+		# gzipping locuszoom input
+		gzip -v ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom 
+		
 		echo ""
 		echo "All finished. Done making regional association plots for ${PHENOTYPE} data."
 		echo ""
@@ -296,8 +303,11 @@ echo "                                             MAKE LOCUSZOOM PLOTS"
 		zcat ${RESULTS} | ${GWASTOOLKITDIR}/SCRIPTS/parseTable.pl --col RSID,P | tail -n +2 >> ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom
 		echo "Plotting variant: ${GENE}"
 		
-			cd ${OUTPUTDIR}
-			${LOCUSZOOM13} --metal ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom --markercol MarkerName --delim space --refgene ${GENE} --flank ${RANGELZ}kb ${LDMAP} theme=publication title="${GENE} in ${PHENOTYPE} (${EXCLUSION})" ${LOCUSZOOM_SETTINGS}
+		cd ${OUTPUTDIR}
+		${LOCUSZOOM13} --metal ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom --markercol MarkerName --delim space --refgene ${GENE} --flank ${RANGELZ}kb ${LDMAP} theme=publication title="${GENE} in ${PHENOTYPE} (${EXCLUSION})" ${LOCUSZOOM_SETTINGS}
+		
+		# gzipping locuszoom input
+		gzip -v ${OUTPUTDIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.QC.locuszoom 
 		
 		echo ""
 		echo "All finished. Done making regional association plots for ${PHENOTYPE} data."
diff --git a/gwastoolkit.plotter.qc.sh b/gwastoolkit.plotter.qc.sh
@@ -83,9 +83,9 @@ echobold "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 echobold "                                          GWASTOOLKIT PLOTTER -- AFTER QC"
 echobold "                              plotting of SNPTEST analysis results after quality control"
 echobold ""
-echobold " Version    : v1.1.4"
+echobold " Version    : v1.1.5"
 echobold ""
-echobold " Last update: 2017-07-07"
+echobold " Last update: 2018-01-24"
 echobold " Written by : Sander W. van der Laan (s.w.vanderlaan-2@umcutrecht.nl)."
 echobold ""
 echobold " Testers    : - Saskia Haitjema (s.haitjema@umcutrecht.nl)"
@@ -129,7 +129,7 @@ else
 	echo ""
 	echo "Plotting reformatted FILTERED data."
 	# what is the basename of the file?
-	RESULTS=${OUTPUT_DIR}/*.summary_results.QC.txt.gz
+	RESULTS=${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.txt.gz
 	FILENAME=$(basename ${RESULTS} .txt.gz)
 	echo "The basename is: "${FILENAME}
 	echo ""
diff --git a/gwastoolkit.plotter.sh b/gwastoolkit.plotter.sh
@@ -83,9 +83,9 @@ echobold "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 echobold "                                               GWASTOOLKIT PLOTTER"
 echobold "                                       plotting of SNPTEST analysis results"
 echobold ""
-echobold " Version    : v1.1.5"
+echobold " Version    : v1.1.6"
 echobold ""
-echobold " Last update: 2017-08-22"
+echobold " Last update: 2018-01-24"
 echobold " Written by : Sander W. van der Laan (s.w.vanderlaan-2@umcutrecht.nl)."
 echobold ""
 echobold " Testers    : - Saskia Haitjema (s.haitjema@umcutrecht.nl)"
@@ -128,7 +128,7 @@ else
 	echo ""
 	echo "Plotting reformatted UNFILTERED data. Processing the following dataset: "
 	# what is the basename of the file?
-	RESULTS=${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}*.summary_results.txt.gz
+	RESULTS=${OUTPUT_DIR}/${STUDY_TYPE}.${ANALYSIS_TYPE}.${REFERENCE}.${PHENOTYPE}.${EXCLUSION}.summary_results.txt.gz
 	echo "* debug * ${RESULTS}"
 	FILENAME=$(basename ${RESULTS} .txt.gz)
 	echo "The basename is: "${FILENAME}

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,3 @@`
`1`	`1`	`RESOURCES`
`2`	`2`	`~$20161102_AEGS_available_phenotypes_covariates.xlsx`
	`3`	`+.DS_Store`