def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
for i in info['APMS_OUT']:
validation.check_file(log, i)
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
for i in info['APMS_OUT']:
validation.check_file(log, i)
return info
def validate_run(self, log, info, exit_code, stdout):
if 'max_rt_diff = self._stdev_max_rt_per_run * tr_data.getStdev(source, target)' in stdout:
raise RuntimeError("No peptides found which are shared between all runs. Try to increase 'alignment_score'.")
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
validation.check_file(log, info['ALIGNMENT_TSV'])
validation.check_file(log, info['ALIGNMENT_YAML'])
out2log = os.path.join(info[Keys.WORKDIR], "feature_alignment.out.txt")
f = open(out2log, "w")
f.write(stdout)
f.close()
info["ALIGNER_STDOUT"] = out2log
# Move out .tr files of pyprophet to be rescue safe
info["TRAFO_FILES"] = []
for fil in info["MPROPHET_TSV"]:
trfile = glob.glob(os.path.dirname(fil) + "/*.tr")
if len(trfile) != 1:
raise RuntimeError("More than one .tr file for " + fil)
basename = os.path.basename(trfile[0])
tgt = os.path.join(info['WORKDIR'], basename)
log.debug("Moved tr file %s into WORKDIR" % basename)
shutil.move(trfile[0], tgt)
info["TRAFO_FILES"].append(tgt)
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, stdout):
log.debug("Cp validation")
# self checked
if "No such file" in stdout:
raise RuntimeError("Inputfile not found")
if "Permission denied" in stdout:
raise RuntimeError("Was not allowed to read inputfile. Need more rights")
# validation util
validation.check_file(log, info["COPY"])
validation.check_exitcode(log, exit_code)
return info
def validate_run(self, log, info, exit_code, stdout):
log.debug("Cp validation")
#self checked
if "No such file" in stdout:
raise RuntimeError("Inputfile not found")
if "Permission denied" in stdout:
raise RuntimeError(
"Was not allowed to read inputfile. Need more rights")
#validation util
validation.check_file(log, info['COPY'])
validation.check_exitcode(log, exit_code)
return info
def validate_run(self, log, info, exit_code, stdout):
if "ERROR [root] Parsing </precursorMz> failed. scan number" in stdout:
raise ValueError("the chosen mzXML %s file contains "
"MS2 spectra without precursor information" % info.get("MZXML")
)
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
info["MD5_SUMS"] = []
for p in info["Q_FILES"]:
validation.check_file(log, p)
md5sum = open(p + ".md5", "r").read().split(" ")[0].strip()
info["MD5_SUMS"].append(md5sum)
return info
def validate_run(self, log, info, exit_code, stdout):
if "ERROR [root] Parsing </precursorMz> failed. scan number" in stdout:
raise ValueError("the chosen mzXML %s file contains "
"MS2 spectra without precursor information" %
info.get("MZXML"))
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
info["MD5_SUMS"] = []
for p in info["Q_FILES"]:
validation.check_file(log, p)
md5sum = open(p + ".md5", "r").read().split(" ")[0].strip()
info["MD5_SUMS"].append(md5sum)
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):
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
base = os.path.join(info[Keys.WORKDIR], os.path.splitext(os.path.basename(info['FEATURETSV']))[0])
info['MPROPHET_TSV'] = base + "_with_dscore_filtered.csv"
validation.check_file(log, info['MPROPHET_TSV'])
prophet_stats = []
for end in ["_full_stat.csv", "_scorer.bin", "_weights.txt", "_report.pdf", "_dscores_top_target_peaks.txt",
"_dscores_top_decoy_peaks.txt"]:
f = base + end
if os.path.exists(f):
prophet_stats.append(f)
if prophet_stats:
info['MPROPHET_STATS'] = prophet_stats
return info
def validate_run(self, log, info, exit_code, stdout):
for line in stdout.splitlines():
# Determined there to be 35792 SWATH windows and in total 6306 MS1 spectra
if 'Determined there to be' in line:
no_swathes = float(line.split()[4])
if no_swathes > 128:
raise RuntimeError('This is a DDA sample, not SWATH!')
if 'is below limit of ' in line:
raise RuntimeError("iRT calibration failed: " + line)
# validation.check_stdout(log,stdout)
validation.check_exitcode(log, exit_code)
validation.check_file(log, info['FEATURETSV'])
if os.path.getsize(info['FEATURETSV']) < 1000:
raise RuntimeError("No peak found, output is empty!")
if 'CHROM_MZML' in info:
#don't use check_xml() because of .gz
validation.check_file(log, info['CHROM_MZML'])
return info
def validate_run(self, log, info, exit_code, stdout):
for line in stdout.splitlines():
# Determined there to be 35792 SWATH windows and in total 6306 MS1 spectra
if 'Determined there to be' in line:
no_swathes = float(line.split()[4])
if no_swathes > 128:
raise RuntimeError('This is a DDA sample, not SWATH!')
if 'is below limit of ' in line:
raise RuntimeError("iRT calibration failed: " + line)
# validation.check_stdout(log,stdout)
validation.check_exitcode(log, exit_code)
validation.check_file(log, info['FEATURETSV'])
if os.path.getsize(info['FEATURETSV']) < 1000:
raise RuntimeError("No peak found, output is empty!")
if 'CHROM_MZML' in info:
#don't use check_xml() because of .gz
validation.check_file(log, info['CHROM_MZML'])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
base = os.path.join(
info[Keys.WORKDIR],
os.path.splitext(os.path.basename(info['FEATURETSV']))[0])
info['MPROPHET_TSV'] = base + "_with_dscore_filtered.csv"
validation.check_file(log, info['MPROPHET_TSV'])
prophet_stats = []
for end in [
"_full_stat.csv", "_scorer.bin", "_weights.txt", "_report.pdf",
"_dscores_top_target_peaks.txt", "_dscores_top_decoy_peaks.txt"
]:
f = base + end
if os.path.exists(f):
prophet_stats.append(f)
if prophet_stats:
info['MPROPHET_STATS'] = prophet_stats
return info
def keys_to_dropbox(log, info, keys, tgt):
if not isinstance(keys, list):
keys = [keys]
for key in keys:
if not info.has_key(key):
raise Exception('key [%s] not found in info for copying to dropbox' % key)
if isinstance(info[key], list):
files = info[key]
else:
files = [info[key]]
for file in files:
try:
log.debug('Copy [%s] to [%s]' % (file, tgt))
shutil.copy(file, tgt)
except:
if validation.check_file(log, file):
log.debug('File [%s] already exists, ignore' % file)
else:
raise Exception('Could not copy [%s] to [%s]' % (file, tgt))
def keys_to_dropbox(log, info, keys, tgt):
if not isinstance(keys, list):
keys = [keys]
for key in keys:
if not info.has_key(key):
raise Exception(
'key [%s] not found in info for copying to dropbox' % key)
if isinstance(info[key], list):
files = info[key]
else:
files = [info[key]]
for file in files:
try:
log.debug('Copy [%s] to [%s]' % (file, tgt))
shutil.copy(file, tgt)
except:
if validation.check_file(log, file):
log.debug('File [%s] already exists, ignore' % file)
else:
raise Exception('Could not copy [%s] to [%s]' %
(file, tgt))
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_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
if info.get('DO_CHROMML_REQUANT', "") != "false":
validation.check_file(log, info['REQUANT_TSV'])
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_file(log, info['MAYUOUT'])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_stdout(log, stdout)
validation.check_exitcode(log, exit_code)
if info.get('DO_CHROMML_REQUANT', "") != "false":
validation.check_file(log, info['REQUANT_TSV'])
return info
def validate_run(self, log, info, exit_code, stdout):
validation.check_exitcode(log, exit_code)
validation.check_file(log, info['MAYUOUT'])
return info
def validate_run(self, log, info, exit_code, stdout):
for f in info['DUMP_MZXML']:
validation.check_file(log, f)
validation.check_exitcode(log, exit_code)
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['ALIGNMENT_MATRIX'])
return info
def validate_run(self, log, info, exit_code, stdout):
for f in info['DUMP_MZXML']:
validation.check_file(log, f)
validation.check_exitcode(log, exit_code)
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['ALIGNMENT_MATRIX'])
return info