def validate_run(self, log, info, exit_code, stdout):
if "Warning - no spectra searched" in stdout:
raise RuntimeError("No spectra in mzXML!")
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):
# Double check "Spectrast finished ..."
if not " without error." in stdout:
raise RuntimeError("SpectraST finished with some error!")
validation.check_exitcode(log, exit_code)
validation.check_file(log, info['SPLIB'])
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):
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):
check_exitcode(log, exit_code)
weblogoexe = info['WEBLOGO']
weblogoinputs = []
for file in self.outfiles:
weblogoinputs += fixStupidGibbsclusterFile(file, file + "out")
commands = runweblogo_on_files(weblogoexe, weblogoinputs)
self.execute_run(log, info, commands)
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 info['RUNRT'] == 'True':
# Spectrast imports sample *whitout error* when no iRTs are found. Thus look for "Comment:" entries without
# iRT= attribute in splib
notenough = set()
for line in open(info['SPLIB']).readlines():
if "Comment:" in line and not "iRT=" in line:
samplename = re.search("RawSpectrum=([^\.]*)\.",
line).group(1)
notenough.add(samplename)
if notenough:
log.error("No/not enough iRT peptides found in sample(s): " +
", ".join(notenough))
#when irt.txt not readable: PEPXML IMPORT: Cannot read landmark table. No RT normalization will be performed.
rtcalibfailed = False
for line in open(info['SPLOG']).readlines():
if "Cannot read landmark table" in line:
log.error("Problem with reading rtkit file %s!" %
info['RTKIT'])
rtcalibfailed = True
# Parse logfile to see whether R^2 is high enough. Example log for failed calibration (line 3 only when <0.9):
# PEPXML IMPORT: RT normalization by linear regression. Found 10 landmarks in MS run "CHLUD_L110830_21".
# PEPXML_IMPORT: Final fitted equation: iRT = (rRT - 1758) / (8.627); R^2 = 0.5698; 5 outliers removed.
# ERROR PEPXML_IMPORT: R^2 still too low at required coverage. No RT normalization performed. Consider...
rsqlow = False
for line in open(info['SPLOG']).readlines():
if "Final fitted equation:" in line:
samplename = prevline.strip().split(" ")[-1]
rsq = line.split()[-4].replace(";", "")
if float(rsq) < float(info['RSQ_THRESHOLD']):
log.error("R^2 of %s is below threshold of %s for %s" %
(rsq, info['RSQ_THRESHOLD'], samplename))
rsqlow = True
else:
log.debug("R^2 of %s is OK for %s" % (rsq, samplename))
else:
prevline = line
# Raise only here to have all errors shown
if rsqlow or rtcalibfailed or notenough:
raise RuntimeError("Error in iRT calibration.")
# Double check "Spectrast finished ..."
if not " without error." in stdout:
raise RuntimeError("SpectraST finished with some error!")
validation.check_exitcode(log, exit_code)
validation.check_file(log, info['SPLIB'])
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):
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
validation.check_file(log, info['SPLIB'])
validation.check_file(log, info['TSV'])
return info