From 05929a88c690e0c7c0fb73db0f990a6530d909c3 Mon Sep 17 00:00:00 2001
From: Beibei Chen <beibei.chen@utsouthwestern.edu>
Date: Thu, 29 Dec 2016 14:59:59 -0600
Subject: [PATCH] memechip framework finished
---
workflow/scripts/runDeepTools.py | 8 ++++----
workflow/scripts/runMemechip.py | 6 ++++--
2 files changed, 8 insertions(+), 6 deletions(-)
diff --git a/workflow/scripts/runDeepTools.py b/workflow/scripts/runDeepTools.py
index 164b0b7..81e02b4 100644
--- a/workflow/scripts/runDeepTools.py
+++ b/workflow/scripts/runDeepTools.py
@@ -51,10 +51,10 @@ def run_signal(files, labels, genome):
bw_commands = []
for f in files:
bw_commands.append("bamCoverage -bs 10 -b "+f+" -o "+f.replace("bam","bw"))
- #work_pool = Pool(min(len(files), 12))
- #work_pool.map(bam2bw_wrapper, bw_commands)
- #work_pool.close()
- #work_pool.join()
+ work_pool = Pool(min(len(files), 12))
+ work_pool.map(bam2bw_wrapper, bw_commands)
+ work_pool.close()
+ 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)
diff --git a/workflow/scripts/runMemechip.py b/workflow/scripts/runMemechip.py
index d0f66f6..4b17dc0 100644
--- a/workflow/scripts/runMemechip.py
+++ b/workflow/scripts/runMemechip.py
@@ -39,8 +39,10 @@ def main():
def run(infile, genome, limit, output)
infile = pybedtools.BedTool(infile)
#genome = twobitreader.TwoBitFile(genome)
- output = open(args.outfile,"w")
+ output = open(output+".fa","w")
rowcount = 1
+ if limit ==-1:
+ limit = len(infile)
for record in infile:
while rowcount <=limit:
rowcount += 1
@@ -56,7 +58,7 @@ def run(infile, genome, limit, output)
SeqIO.write(newfa,output+".fa","fasta")
output.close()
#Call memechip
- meme_command = "meme-chip -oc "+output+" -meme-minw 5 -meme-maxw 15 -meme-nmotifs 10"
+ meme_command = "meme-chip -oc "+output+"_memechip"+" -meme-minw 5 -meme-maxw 15 -meme-nmotifs 10 "+output+".fa"
p = subprocess.Popen(meme_command, shell=True)
p.communicate()
--
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