/usr/lib/python2.7/dist-packages/metastudentPkg/BlastWrapper.py is in metastudent 2.0.1-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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Created on May 18, 2010
@author: tobiashamp
'''
class blastallParameters:
def __init__(self):
self.hValue = ""
self.numberOfCPUs = 1
def setBlastExePath(self, path):
self.blastExePath = path
def setOutputFilePath(self, path):
self.outputFilePath = path
def getOutputFilePath(self):
return self.outputFilePath
def setInputFilePath(self, path):
self.inputFilePath = path
def getBlastExePath(self):
return self.blastExePath
def getInputFilePath(self):
return self.inputFilePath
def setBlastDatabasePath(self, path):
self.blastDatabasePath = path
def getBlastDatabasePath(self):
return self.blastDatabasePath
def setEValue(self, value):
self.eValue = value
def getEValue(self):
return self.eValue
def setJ(self, value):
self.j = value
def getJ(self):
return self.j
def setB(self, value):
self.B = value
def getB(self):
return self.B
def setV(self, value):
self.v = value
def getV(self):
return self.v
def createBlastPGPCommand(blastParameters):
returnString = blastParameters.getBlastExePath()
returnString += " -i " + blastParameters.getInputFilePath() + \
" -o " + blastParameters.getOutputFilePath() + \
" -d " + blastParameters.getBlastDatabasePath() + \
" -e " + str(blastParameters.getEValue()) + \
" -j " + str(blastParameters.getJ()) + \
" -b " + str(blastParameters.getB()) + \
" -v " + str(blastParameters.getV()) + \
" 1>" + blastParameters.getOutputFilePath()+".out" + \
" 2>" + blastParameters.getOutputFilePath()+".err"
return returnString
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