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Shell handles input file corrctly

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bchen4
bchen4 committed Mar 24, 2015
1 parent 46d96e3 commit d8521c58af721d8dfe43c955125413b029c19189
Showing with 7 additions and 7 deletions.
  1. +3 −3 lib/Enrich.py
  2. +3 −3 lib/runR1.sh
  3. +1 −1 pipeclip.py
@@ -130,7 +130,7 @@ def KMvalue_test(clip,mutations,chr,chrlen):
try:
K = poswig[item.start]
except:
log.warning("Did not find mutation in poswig")
#log.warning("Did not find mutation in poswig")
continue
elif strand == "-":
try:
@@ -161,7 +161,7 @@ def mutationEnrich(clip,threshold=0.01):
mutations = []
total_test = 0
for chr,chrlen in clip.refInfo:
logging.debug(chr)
#logging.debug(chr)
try:
mufile = open(clip.outprefix+"."+chr+".mutations.bed")
except:
@@ -371,7 +371,7 @@ def clusterEnrich_outsource(clip, threshold=0.01):
#Call R code and get result
#epsilon = [0.01,0.15,0.1]
#step = [0.1,0.08,0.05]
sh_args = ['sh','runR1.sh',cluster_filename,str(threshold)]
sh_args = ['sh','lib/runR1.sh',cluster_filename,str(threshold)]
p = subprocess.Popen(sh_args)
stdout_value = p.communicate()[0]

@@ -1,6 +1,6 @@
#!/bin/sh
filename="../test/test.merge"
pvalue = $2
filename=$1
pvalue=$2
#declare -a epsilon
#declare -a steps
epsilon=(0.01 0.15 0.1)
@@ -45,7 +45,7 @@ do
echo
else
#echo "$e,$s"
Rscript ZTNB_tryCatch.R $filename $pvalue $e $s
Rscript lib/ZTNB_tryCatch.R $filename $pvalue $e $s
fi
#echo "$filename.$count"
count=$((count+1))
@@ -30,7 +30,7 @@ def prepare_argparser():

def runPipeClip(infile,control,outputPrefix,matchLength,mismatch,rmdup,fdrEnrichedCluster,clipType,fdrReliableMutation,species):
myClip = CLIP.CLIP(infile,outputPrefix)
contrlFlag = False
controlFlag = False
if control != None:
controlClip = CLIP.CLIP(control,outputPrefix+"Control")
logging.info("Start to run")

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