From be305349bd66dc8d50fa45c37f0be3997cf912f3 Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Tue, 27 Dec 2016 16:29:18 -0600
Subject: [PATCH] runDiffBind output bed format
---
workflow/main.nf | 2 ++
workflow/scripts/runDeepTools.py | 6 +++---
workflow/scripts/runDiffBind.R | 8 ++++++--
3 files changed, 11 insertions(+), 5 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index d7b7829..2766722 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -24,6 +24,8 @@ process peakanno {
script:
"""
module load R/3.2.1-intel
+ module load deeptools/2.5.3
+ module load python/2.7.x-anaconda
python $baseDir/scripts/process.py
#Rscript /project/BICF/BICF_Core/bchen4/chipseq_analysis/workflow/scripts/runchipseeker.R
"""
diff --git a/workflow/scripts/runDeepTools.py b/workflow/scripts/runDeepTools.py
index dad0cec..164b0b7 100644
--- a/workflow/scripts/runDeepTools.py
+++ b/workflow/scripts/runDeepTools.py
@@ -57,9 +57,9 @@ def run_signal(files, labels, genome):
#work_pool.join()
cm_command = "computeMatrix scale-regions -R "+gene_bed+" -a 3000 -b 3000 --regionBodyLength 5000 --skipZeros -S *.bw -o samples.deeptools_generegionscalematrix.gz"
- p = subprocess.Popen(cm_command, shell=True)
- p.communicate()
- hm_command = "plotHeatmap -m samples.deeptools_generetionscalematrix.gz -out samples.deeptools_readsHeatmap.png"
+ #p = subprocess.Popen(cm_command, shell=True)
+ #p.communicate()
+ hm_command = "plotHeatmap -m samples.deeptools_generegionscalematrix.gz -out samples.deeptools_readsHeatmap.png"
p = subprocess.Popen(hm_command, shell=True)
p.communicate()
diff --git a/workflow/scripts/runDiffBind.R b/workflow/scripts/runDiffBind.R
index c4cffa0..266fea7 100644
--- a/workflow/scripts/runDiffBind.R
+++ b/workflow/scripts/runDiffBind.R
@@ -1,7 +1,8 @@
library("DiffBind")
#build dba object from sample sheet and do analysis
-data <- dba(sampleSheet="samplesheet.csv")
+args <- commandArgs(TRUE)
+data <- dba(sampleSheet=args[1])
data <- dba.count(data)
data <- dba.contrast(data, minMembers = 2, categories=DBA_CONDITION)
data <- dba.analyze(data)
@@ -23,8 +24,11 @@ write.table(as.data.frame(normcount),"diffbind.normcount.txt",sep="\t",quote=F,r
for (i in c(1:length(data$contrasts)))
{
contrast_name = paste(data$contrasts[[i]]$name1,"vs",
- data$contrasts[[i]]$name2,"diffbind.xls",sep="_")
+ contrast_bed_name = paste(data$contrasts[[i]]$name1,"vs",
+ data$contrasts[[i]]$name2,"diffbind.bed",sep="_")
report <- dba.report(data, contrast=i, th=1, bCount=TRUE)
write.table(as.data.frame(report),contrast_name,sep="\t",quote=F,row.names=F)
+ write.table(as.data.frame(report),contrast_bed_name,sep="\t",quote=F,row.names=F, col.names=F)
+
}
--
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