remove annotate peak vennpie and update test.

workflow/scripts/annotate_peaks.R

@@ -40,17 +40,26 @@ design <- read.csv(design_file, sep ='\t')
 files <- as.list(as.character(design$Peaks))
 names(files) <- design$Condition
 
+# Granges of files
+
+peaks <- lapply(files, readPeakFile, as = "GRanges", header = FALSE)
+peakAnnoList <- lapply(peaks, annotatePeak, TxDb=txdb, annoDb=annodb, tssRegion=c(-3000, 3000), verbose=FALSE)
+
+column_names <- c("chr", "start", "end", "width", "strand_1", "name", "score", "strand", "signalValue",
+                  "pValue", "qValue", "peak", "annotation", "geneChr", "geneStart", "geneEnd",
+                  "geneLength" ,"geneStrand", "geneId", "transcriptId", "distanceToTSS",
+                  "ENSEMBL", "symbol", "geneName")
 
-peakAnnoList <- lapply(files, annotatePeak, TxDb=txdb, annoDb=annodb, tssRegion=c(-3000, 3000), verbose=FALSE)
 for(index in c(1:length(peakAnnoList))) {
-  filename <- paste(names(files)[index],".chipseeker_annotation.csv",sep="")
-  write.table(as.data.frame(peakAnnoList[[index]]),filename,sep=",",quote=F)
+  filename <- paste(names(peaks)[index], ".chipseeker_annotation.csv", sep="")
+  df <- as.data.frame(peakAnnoList[[index]])
+  colnames(df) <- column_names
+  write.table(df[ , !(names(df) %in% c('strand_1'))], filename, sep="," ,quote=F, row.names=F)
 
   # Draw individual plots
 
   # Define names of Plots
   pie_name <- paste(names(files)[index],".chipseeker_pie.pdf",sep="")
-  vennpie_name <- paste(names(files)[index],".chipseeker_vennpie.pdf",sep="")
   upsetplot_name <- paste(names(files)[index],".chipseeker_upsetplot.pdf",sep="")
 
   # Pie Plots
@@ -58,11 +67,6 @@ for(index in c(1:length(peakAnnoList))) {
   plotAnnoPie(peakAnnoList[[index]])
   dev.off()
 
-  # Venn Diagrams
-  pdf(vennpie_name)
-  vennpie(peakAnnoList[[index]])
-  dev.off()
-
   # Upset Plot
   pdf(upsetplot_name)
   upsetplot(peakAnnoList[[index]])

workflow/tests/test_annotate_peaks.py

@@ -13,8 +13,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 @pytest.mark.singleend
 def test_annotate_peaks_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_pie.pdf'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_pie.pdf'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_pie.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_upsetplot.pdf'))
     annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.csv'
     assert os.path.exists(annotation_file)
     assert utils.count_lines(annotation_file) == 152839
@@ -23,8 +22,7 @@ def test_annotate_peaks_singleend():
 @pytest.mark.pairedend
 def test_annotate_peaks_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LRF.chipseeker_pie.pdf'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LRF.chipseeker_pie.pdf'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LRF.chipseeker_pie.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LRF.chipseeker_upsetplot.pdf'))
     annotation_file = test_output_path + 'ENCSR217LRF.chipseeker_annotation.csv'
     assert os.path.exists(annotation_file)
     assert utils.count_lines(annotation_file) == 25390