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Commit ad8a4c25 authored by Venkat Malladi's avatar Venkat Malladi
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Make csv to tsv.

parent 29ea563e
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1 merge request!18Resolve "Add in current chip-analysis functionality."
Pipeline #2784 failed with stages
in 19 hours, 11 minutes, and 28 seconds
......@@ -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
......
......@@ -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
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