From ad8a4c2586a3c5f7c97c426b348e779b749653ec Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Thu, 10 Jan 2019 10:08:17 -0600
Subject: [PATCH] Make csv to tsv.
---
workflow/scripts/annotate_peaks.R | 4 ++--
workflow/tests/test_annotate_peaks.py | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/workflow/scripts/annotate_peaks.R b/workflow/scripts/annotate_peaks.R
index 135d1b6..c15ba69 100644
--- a/workflow/scripts/annotate_peaks.R
+++ b/workflow/scripts/annotate_peaks.R
@@ -51,10 +51,10 @@ column_names <- c("chr", "start", "end", "width", "strand_1", "name", "score", "
"ENSEMBL", "symbol", "geneName")
for(index in c(1:length(peakAnnoList))) {
- filename <- paste(names(peaks)[index], ".chipseeker_annotation.csv", sep="")
+ filename <- paste(names(peaks)[index], ".chipseeker_annotation.tsv", 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)
+ write.table(df[ , !(names(df) %in% c('strand_1'))], filename, sep="\t" ,quote=F, row.names=F)
# Draw individual plots
diff --git a/workflow/tests/test_annotate_peaks.py b/workflow/tests/test_annotate_peaks.py
index fa5c241..692ddce 100644
--- a/workflow/tests/test_annotate_peaks.py
+++ b/workflow/tests/test_annotate_peaks.py
@@ -14,7 +14,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
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_upsetplot.pdf'))
- annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.csv'
+ annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.tsv'
assert os.path.exists(annotation_file)
assert utils.count_lines(annotation_file) == 152840
@@ -23,6 +23,6 @@ def test_annotate_peaks_singleend():
def test_annotate_peaks_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.chipseeker_pie.pdf'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.chipseeker_upsetplot.pdf'))
- annotation_file = test_output_path + 'ENCSR729LGA.chipseeker_annotation.csv'
+ annotation_file = test_output_path + 'ENCSR729LGA.chipseeker_annotation.tsv'
assert os.path.exists(annotation_file)
assert utils.count_lines(annotation_file) == 25391
--
GitLab