def validate_run(self, log, info, run_code, out): if "No decoys with label DECOY_ were found" in out: raise RuntimeError("No DECOY_s found in fasta. Please use other fasta!") validation.check_stdout(log, out) validation.check_exitcode(log, run_code) validation.check_xml(log, info[Keys.PEPXML]) return info
def validate_run(self, log, info, exit_code, stdout): validation.check_stdout(log,stdout) validation.check_exitcode(log, exit_code) validation.check_file(log, info['SPLIB']) validation.check_file(log, info['TSV']) validation.check_xml(log, info['TRAML']) return info
def validate_run(self, log, info, exit_code, out): validation.check_exitcode(log, exit_code) if 'Valid models = 0' in out: raise RuntimeError('No valid model found') validation.check_xml(log, info[Keys.PEPXML]) return info
def validate_run(self, log, info, run_code, out): for line in out.splitlines(): if "OpenMS peak type estimation indicates that this is not profile data!" in line: raise RuntimeError("Found centroid data but LFQ must be run on profile mode data!") validation.check_stdout(log, out) validation.check_exitcode(log, run_code) validation.check_xml(log, info['FEATUREXML']) return info
def validate_run(self, log, info, run_code, out): if "No decoys with label DECOY_ were found" in out: raise RuntimeError( "No DECOY_s found in fasta. Please use other fasta!") validation.check_stdout(log, out) validation.check_exitcode(log, run_code) validation.check_xml(log, info[Keys.PEPXML]) return info
def validate_run(self, log, info, exit_code, stdout): if exit_code == -8: raise RuntimeError("iProphet failed most probably because too few peptides were found in the search before") for line in stdout.splitlines(): if 'fin: error opening' in line: raise RuntimeError("Could not read the input file " + line) validation.check_exitcode(log, exit_code) validation.check_xml(log, info[Keys.PEPXML]) return info
def validate_run(self, log, info, exit_code, stdout): validation.check_exitcode(log, exit_code) for msg in ['Error:','did not find any InterProphet results in input data!', 'no data - quitting', 'WARNING: No database referenced']: if msg in stdout: raise RuntimeError('ProteinProphet error [%s]' % msg) validation.check_xml(log, info[Keys.PROTXML]) return info
def validate_run(self, log, info, exit_code, stdout): if "Warning - no spectra searched" in stdout: raise RuntimeError("No spectra in mzXML!") if "CometMemAlloc" in stdout: #print to stdout to reach gUSE rescue functionality. ugly, no? print "MemoryError" raise RuntimeError("The job run out of RAM!") check_stdout(log,stdout) check_exitcode(log, exit_code) check_xml(log, info[Keys.PEPXML]) return info
def validate_run(self, log, info, exit_code, stdout): validation.check_exitcode(log, exit_code) for msg in [ 'Error:', 'did not find any InterProphet results in input data!', 'no data - quitting', 'WARNING: No database referenced' ]: if msg in stdout: raise RuntimeError('ProteinProphet error [%s]' % msg) validation.check_xml(log, info[Keys.PROTXML]) return info
def validate_run(self, log, info, exit_code, stdout): check_exitcode(log, exit_code) check_xml(log, info[Keys.PEPXML]) #https://groups.google.com/forum/#!topic/spctools-discuss/dV8LSaE60ao shutil.move(info[Keys.PEPXML], info[Keys.PEPXML]+'.broken') fout = open(info[Keys.PEPXML],'w') for line in open(info[Keys.PEPXML]+'.broken').readlines(): if 'spectrumNativeID' in line: line = re.sub('spectrumNativeID="[^"]*"', '', line) fout.write(line) fout.close() return info
def validate_run(self, log, info, exit_code, stdout): if "Warning - no spectra searched" in stdout: raise RuntimeError("No spectra in mzXML!") if "CometMemAlloc" in stdout: #print to stdout to reach gUSE rescue functionality. ugly, no? print "MemoryError" raise RuntimeError("The job run out of RAM!") check_stdout(log,stdout) if exit_code: log.warn("exit_code is %s", exit_code) mzxml = info[Keys.MZXML] log.warn("maybe the input file %s does not exist any more. check this !" % mzxml) check_exitcode(log, exit_code) check_xml(log, info[Keys.PEPXML]) return info
def validate_run(self, log, info, exit_code, stdout): if "Warning - no spectra searched" in stdout: raise RuntimeError("No spectra in mzXML!") if "CometMemAlloc" in stdout: #print to stdout to reach gUSE rescue functionality. ugly, no? print "MemoryError" raise RuntimeError("The job run out of RAM!") check_stdout(log, stdout) if exit_code: log.warn("exit_code is %s", exit_code) mzxml = info[Keys.MZXML] log.warn( "maybe the input file %s does not exist any more. check this !" % mzxml) check_exitcode(log, exit_code) check_xml(log, info[Keys.PEPXML]) return info
def validate_run(self, log, info, exit_code, stdout): validation.check_exitcode(log, exit_code) validation.check_stdout(log, stdout) validation.check_xml(log, info[Keys.PEPXML]) return info
def validate_run(self, log, info, run_code, out): validation.check_exitcode(log, run_code) validation.check_file(log, info['PROTCSV']) validation.check_file(log, info['PEPCSV']) validation.check_xml(log, info['CONSENSUSXML']) return info
def validate_run(self, log, info, exit_code, stdout): validation.check_exitcode(log, exit_code) validation.check_xml(log, info['PROTXML']) return info
def validate_run(self, log, info, exit_code, stdout): validation.check_exitcode(log, exit_code) validation.check_stdout(log,stdout) validation.check_xml(log, info[Keys.PEPXML]) return info