""" chainsaw.py: CCP4 GUI Project Copyright (C) 2010 University of York This library is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License version 3, modified in accordance with the provisions of the license to address the requirements of UK law. You should have received a copy of the modified GNU Lesser General Public License along with this library. If not, copies may be downloaded from http://www.ccp4.ac.uk/ccp4license.php This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. """ import os from core.CCP4PluginScript import CPluginScript class chainsaw(CPluginScript): TASKMODULE = 'molecular replacement' # Where this plugin will appear on gui TASKTITLE = 'edit search model' # A short title for gui menu TASKNAME = 'chainsaw' # Task name - should be same as class name TASKVERSION= 0.1 # Version of this plugin MAINTAINER = 'ronan.keegan@stfc.ac.uk' PERFORMANCECLASS = 'CAtomCountPerformance' # used by the base class startProcess() TASKCOMMAND = 'chainsaw' # The command to run the executable def makeCommandAndScript(self): print 'chainsaw.makeCommandAndScript' if self.container.inputData.XYZIN.isSelectionSet(): xyzin_file = os.path.join(self.getWorkDirectory(),"XYZIN_sel.pdb") self.container.inputData.XYZIN.getSelectedAtomsPdbFile(xyzin_file) else: xyzin_file = str(self.container.inputData.XYZIN) self.appendCommandLine(['XYZIN',xyzin_file]) self.appendCommandLine(['ALIGNIN',self.inputAlignmentFileName]) self.appendCommandLine(['XYZOUT',self.container.outputData.XYZOUT.fullPath]) ### keywords self.appendCommandScript('MODE %s' % self.container.controlParameters.MODE) self.appendCommandScript('END') def processInputFiles(self): self.cryst1card = None with open(str(self.container.inputData.XYZIN.fullPath),'r') as inputFile: lines = inputFile.readlines() for line in lines: if line.startswith('CRYST1'): self.cryst1card = line # Ensure correct alignment file extension and reorder file if target is not first formt,idList = self.container.inputData.ALIGNIN.identifyFile() ext = { 'unknown' : 'aln', 'clustal' : 'aln' , 'fasta' : 'fas', 'pir' : 'pir' , 'phylip' : 'phy' }.get(formt,'aln') self.inputAlignmentFileName = os.path.normpath(os.path.join(self.getWorkDirectory(),'tempAlignment.'+ext)) #print 'inputAlignmentFileName',self.inputAlignmentFileName,'TARGETINDEX',self.container.controlParameters.TARGETINDEX if self.container.controlParameters.TARGETINDEX.isSet() and self.container.controlParameters.TARGETINDEX != 0: formt,idList = self.container.inputData.ALIGNIN.identifyFile() self.container.inputData.ALIGNIN.convertFormat(formt,self.inputAlignmentFileName,reorder='reverse') else: # Forcing the file extension to chainsaw requirement import shutil shutil.copyfile(self.container.inputData.ALIGNIN.__str__(), self.inputAlignmentFileName) return CPluginScript.SUCCEEDED def processOutputFiles(self): if self.cryst1card is not None: import os tmpFilename = str(self.container.outputData.XYZOUT.fullPath)+'_tmp' os.rename(str(self.container.outputData.XYZOUT.fullPath), tmpFilename) with open(tmpFilename,'r') as inputFile: lines = inputFile.readlines() with open(str(self.container.outputData.XYZOUT.fullPath),'w') as outputFile: outputFile.write(self.cryst1card) for line in lines: outputFile.write(line) self.container.outputData.XYZOUT.subType=2 self.container.outputData.XYZOUT.annotation = 'Chainsawed model coordinates' # sanity check that chainsaw has produced something # -1 means we have not managed to get value out of log file self.container.outputData.NO_DELETED = -1 self.container.outputData.NO_CONSERVED = -1 self.container.outputData.NO_MUTATED = -1 logText = self.logFileText() pyListLogLines = logText.split("\n") for j, pyStrLine in enumerate(pyListLogLines): if "conserved" in pyStrLine and "mutated" in pyStrLine: self.container.outputData.NO_DELETED = int(pyStrLine.split()[0]) self.container.outputData.NO_CONSERVED = int(pyStrLine.split()[2]) self.container.outputData.NO_MUTATED = int(pyStrLine.split()[4]) if self.container.outputData.NO_CONSERVED > -1 and self.container.outputData.NO_MUTATED > -1: self.container.outputData.NUMRES_MODEL = self.container.outputData.NO_CONSERVED + self.container.outputData.NO_MUTATED self.container.outputData.SEQID = float(self.container.outputData.NO_CONSERVED) / float(self.container.outputData.NUMRES_MODEL) self.container.saveDataToXml(self.makeFileName( 'PROGRAMXML' )) # Set a performance parameter mostly used in i2 testing self.container.outputData.PERFORMANCE.setFromPdbDataFile(self.container.outputData.XYZOUT) #print 'PERFORMANCE',self.container.outputData.PERFORMANCE.nAtoms,self.container.outputData.PERFORMANCE.nResidues return CPluginScript.SUCCEEDED #====================================================== # PLUGIN TESTS # See Python documentation on unittest module import unittest class testchainsaw(unittest.TestCase): def setUp(self): from core import CCP4Modules self.app = CCP4Modules.QTAPPLICATION() # make all background jobs wait for completion # this is essential for unittest to work CCP4Modules.PROCESSMANAGER().setWaitForFinished(10000) def tearDown(self): from core import CCP4Modules CCP4Modules.PROCESSMANAGER().setWaitForFinished(-1) def test_1(self): from core import CCP4Modules, CCP4Utils import os workDirectory = CCP4Utils.getTestTmpDir() # this needs to agree with name attribute below logFile = os.path.join(workDirectory,'chainsaw_test1.log') # Delete any existing log file if os.path.exists(logFile): os.remove(logFile) self.wrapper = chainsaw(parent=CCP4Modules.QTAPPLICATION(),name='chainsaw_test1',workDirectory=workDirectory) self.wrapper.container.loadDataFromXml(os.path.join(CCP4Utils.getCCP4I2Dir(),'wrappers','chainsaw','test_data','chainsaw_test1.data.xml')) self.wrapper.setWaitForFinished(1000000) pid = self.wrapper.process() self.wrapper.setWaitForFinished(-1) if len(self.wrapper.errorReport)>0: print self.wrapper.errorReport.report() #self.assertTrue(os.path.exists(logFile),'No log file found') def TESTSUITE(): suite = unittest.TestLoader().loadTestsFromTestCase(testchainsaw) return suite def testModule(): suite = TESTSUITE() unittest.TextTestRunner(verbosity=2).run(suite)