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Commit cddbd280 authored by Aflitos, Saulo Alves's avatar Aflitos, Saulo Alves
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2012-10-25_00_55_01_02_00 :: 1 :: M => 1

parent 933c8956
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pipeline/progs/Quake/bin/quake.py
+ 83
− 56
View file @ cddbd280
......@@ -530,74 +530,101 @@ def runAnalysis(setup):
if key == 'data': continue
print '%s :: correcting :: %-16s: %s' % ( listFileName, key, setup[key] )
resp = []
if model_gc:
# run correct C++ code
listFileNameCmd = "-f "
if readsf:
listFileNameCmd = "-r "
listFileNameCmd += listFileName
#cmd = '%s/correct %s %s -m %s -a cutoffs.gc.txt -q %d' % (quake_dir, correct_options, listFileNameCmd, ctsf, quality_scale)
cmd = '%s/correct %s %s -m %s -a cutoffs.gc.txt -q %d' % ('/home/assembly/bin/Quake/bin', correct_options, listFileNameCmd, ctsf, quality_scale)
allOk = True
nfo = data[listFileName]
if nfo is not None:
#data[newListFileName][fileTmpPath].append( [ outFile, dstFile ] )
for fileTmpPath in nfo:
for outFiles in nfo[fileTmpPath]:
tmpFile, dstFile, compulsory = outFiles
if compulsory:
if not os.path.exists(dstFile):
allOk = False
print "%s :: correcting :: %s" % ( listFileName, cmd )
if os.path.exists(dstFile + '.ok'):
allOk = False
p = subprocess.Popen(cmd, shell=True)
pid, status = os.waitpid(p.pid, 0)
print "%s :: correcting :: finished %d" % ( listFileName, status )
resp = [data, listFileName, status]
if allOk:
print '%s :: correcting :: %-16s: %s : !! already corrected. skipping !!' % ( listFileName, key, setup[key] )
return [data, listFileName, 0]
else:
listFileNameCmd = "-f "
if readsf:
listFileNameCmd = "-r "
listFileNameCmd += listFileName
# run correct C++ code
#cmd = '%s/correct %s %s -q %d -b bithash.bh' % (quake_dir, correct_options, listFileNameCmd, quality_scale)
cmd = '%s/correct %s %s -b bithash.bh -q %d' % ('/home/assembly/bin/Quake/bin', correct_options, listFileNameCmd, quality_scale)
print "%s :: correcting :: %s" % ( listFileName, cmd )
p = subprocess.Popen(cmd, stdout=sys.stdout, stderr=sys.stderr, shell=True)
pid, status = os.waitpid(p.pid, 0)
#pid, status = 123, 0
print "%s :: correcting :: finished %d" % ( listFileName, status )
resp = [data, listFileName, status]
resp = []
if model_gc:
# run correct C++ code
listFileNameCmd = "-f "
if readsf:
listFileNameCmd = "-r "
listFileNameCmd += listFileName
#cmd = '%s/correct %s %s -m %s -a cutoffs.gc.txt -q %d' % (quake_dir, correct_options, listFileNameCmd, ctsf, quality_scale)
cmd = '%s/correct %s %s -m %s -a cutoffs.gc.txt -q %d' % ('/home/assembly/bin/Quake/bin', correct_options, listFileNameCmd, ctsf, quality_scale)
print "%s :: correcting :: %s" % ( listFileName, cmd )
p = subprocess.Popen(cmd, shell=True)
pid, status = os.waitpid(p.pid, 0)
data, listFileName, response = resp
print "%s :: correcting :: finished %d" % ( listFileName, status )
resp = [data, listFileName, status]
print '%s :: callback :: response (%d)' % ( listFileName, response )
else:
listFileNameCmd = "-f "
if readsf:
listFileNameCmd = "-r "
listFileNameCmd += listFileName
# run correct C++ code
#cmd = '%s/correct %s %s -q %d -b bithash.bh' % (quake_dir, correct_options, listFileNameCmd, quality_scale)
cmd = '%s/correct %s %s -b bithash.bh -q %d' % ('/home/assembly/bin/Quake/bin', correct_options, listFileNameCmd, quality_scale)
print "%s :: correcting :: %s" % ( listFileName, cmd )
p = subprocess.Popen(cmd, stdout=sys.stdout, stderr=sys.stderr, shell=True)
pid, status = os.waitpid(p.pid, 0)
#pid, status = 123, 0
print "%s :: correcting :: finished %d" % ( listFileName, status )
resp = [data, listFileName, status]
data, listFileName, response = resp
print '%s :: callback :: response (%d)' % ( listFileName, response )
if response != 0:
print "%s :: callback :: finished with value %d" % (listFileName, response)
#sys.exit(response)
return resp
nfo = data[listFileName]
if nfo is not None:
#data[newListFileName][fileTmpPath].append( [ outFile, dstFile ] )
for fileTmpPath in nfo:
for outFiles in nfo[fileTmpPath]:
tmpFile, dstFile, compulsory = outFiles
if compulsory:
if not os.path.exists(tmpFile):
print "did not create tmp file: %s" % tmpFile
print "creating dummy"
with open(tmpFile, 'w') as t:
t.write('@dummy\n')
t.write('N\n')
t.write('+dummy\n')
t.write('%s\n' % chr(quality_scale))
if os.path.exists(tmpFile):
print "%s :: callback :: moving %s to %s" % ( listFileName, tmpFile, dstFile )
try:
shutil.copy(tmpFile, dstFile)
except:
return [data, listFileName, 333]
with open(dstFile + ".ok", "w") as d:
d.write("ok")
if response != 0:
print "%s :: callback :: finished with value %d" % (listFileName, response)
#sys.exit(response)
return resp
nfo = data[listFileName]
if nfo is not None:
#data[newListFileName][fileTmpPath].append( [ outFile, dstFile ] )
for fileTmpPath in nfo:
for outFiles in nfo[fileTmpPath]:
tmpFile, dstFile, compulsory = outFiles
if compulsory:
if not os.path.exists(tmpFile):
print "did not create tmp file: %s" % tmpFile
print "creating dummy"
with open(tmpFile, 'w') as t:
t.write('@dummy\n')
t.write('N\n')
t.write('+dummy\n')
t.write('%s\n' % chr(quality_scale))
if os.path.exists(tmpFile):
print "%s :: callback :: moving %s to %s" % ( listFileName, tmpFile, dstFile )
shutil.copy(tmpFile, dstFile)
return [data, listFileName, 0]
def preexec_function():
signal.signal(signal.SIGINT, signal.SIG_IGN)
......
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