def test_fdr(self):
iprob, fdr = get_iprob_for_fdr("0.004",
"mayu-mFDR",
mayuout='mayuout_main_1.07.csv')
assert iprob == 0.916488
iprob, fdr = get_iprob_for_fdr("0.025",
"mayu-pepFDR",
mayuout='mayuout_main_1.07.csv')
assert iprob == 0.75728
iprob, fdr = get_iprob_for_fdr("0.05",
"mayu-protFDR",
mayuout='mayuout_main_1.07.csv')
assert iprob == 0.803986
iprob, fdr = get_iprob_for_fdr("0.025",
"iprophet-pepFDR",
pepxml="iprophet.pep.xml")
assert iprob == 0.6524
self.assertRaises(RuntimeError,
get_iprob_for_fdr,
"0.1234",
"iprophet-pepFDR",
pepxml="iprophet.pep.xml")
def test_fdr(self):
iprob, fdr = get_iprob_for_fdr("0.004", "mayu-mFDR", mayuout='mayuout_main_1.07.csv')
assert iprob == 0.916488
iprob, fdr = get_iprob_for_fdr("0.025", "mayu-pepFDR", mayuout='mayuout_main_1.07.csv')
assert iprob == 0.75728
iprob, fdr = get_iprob_for_fdr("0.05", "mayu-protFDR", mayuout='mayuout_main_1.07.csv')
assert iprob == 0.803986
iprob, fdr = get_iprob_for_fdr("0.025", "iprophet-pepFDR", pepxml="iprophet.pep.xml")
assert iprob == 0.6524
self.assertRaises(RuntimeError, get_iprob_for_fdr, "0.1234", "iprophet-pepFDR", pepxml="iprophet.pep.xml")
def prepare_run(self, log, info):
wd = info[Keys.WORKDIR]
# get iProb corresponding FDR for IDFilter
info['IPROB'], info['FDR'] = get_iprob_for_fdr(info['FDR_CUTOFF'], info['FDR_TYPE'], mayuout=info.get('MAYUOUT'),
pepxml=info[Keys.PEPXML])
# required because openbis requires prot.xml and openms protXML
peplink = os.path.join(wd, 'iprophet.pepXML')
os.symlink(info[Keys.PEPXML], peplink)
info[Keys.PEPXML] = peplink
info['MZNAME'] = os.path.splitext(os.path.basename(info[Keys.MZXML]))[0]
tpl = os.path.join(wd, 'part1_pp_ff.toppas')
templates.read_mod_write(info, templates.get_tpl_of_class(self), tpl)
#add toppas file path, will be added in dropbox
info["TOPPASFILES"] = tpl
rawfeatxml = os.path.join(wd, 'TOPPAS_out/012-IDConflictResolver/*.featureXML')
info['FEATUREXML'] = os.path.join(wd, os.path.splitext(os.path.basename(info[Keys.MZXML]))[0] + '.featureXML')
command = 'ExecutePipeline -in %s -out_dir %s | grep -v "^WARNING" && chmod -R g+w %s && ' \
'mv -v %s %s' % (
tpl, wd, wd,
rawfeatxml, info['FEATUREXML'])
return info, command
def prepare_run(self, log, info):
if isinstance(info[Keys.PEPXML], list):
raise RuntimeError("This ProteinProphet only takes one iProphet inputfile!")
info['IPROB'],info['FDR'] = get_iprob_for_fdr(info['FDR_CUTOFF'], info['FDR_TYPE'], mayuout=info.get('MAYUOUT'),
pepxml=info[Keys.PEPXML])
info['PROTEINPROPHET'] = 'IPROPHET MINPROB%s' % info['IPROB']
wd = info[Keys.WORKDIR]
info['PROTXML'] = os.path.join(wd, 'ProteinProphet.prot.xml')
exe = info.get(Keys.EXECUTABLE, 'ProteinProphet')
command = '%s %s %s %s' % (exe, info[Keys.PEPXML], info['PROTXML'], info['PROTEINPROPHET'])
return info, command
def prepare_run(self, log, info):
# symlink the pepxml and mzxml files first into a single directory
peplink = os.path.join(info[Keys.WORKDIR], os.path.basename(info[Keys.PEPXML]))
log.debug('create symlink [%s] -> [%s]' % (info[Keys.PEPXML], peplink))
os.symlink(info[Keys.PEPXML], peplink)
if isinstance(info[Keys.MZXML], list):
mzxmlslinks = info[Keys.MZXML]
else:
mzxmlslinks = [info[Keys.MZXML]]
for f in mzxmlslinks:
dest = os.path.join(info[Keys.WORKDIR], os.path.basename(f))
log.debug('create symlink [%s] -> [%s]' % (f, dest))
os.symlink(f, dest)
info['SPLOG'] = os.path.join(info[Keys.WORKDIR], 'spectrast.log')
# get iProb corresponding FDR for IDFilter
info['IPROB'], info['FDR'] = get_iprob_for_fdr(info['FDR_CUTOFF'], info['FDR_TYPE'],
mayuout=info.get('MAYUOUT'),
pepxml=info.get(Keys.PEPXML))
if info.get("RUNRT") == "True":
rtcorrect = "-c_IRT%s -c_IRR" % info['RTKIT']
else:
rtcorrect = ""
rtcalib_base = os.path.join(info[Keys.WORKDIR], 'RTcalib')
rtcalib = rtcalib_base + '.splib'
consensustype = ""
if info['CONSENSUS_TYPE'] == "Consensus":
consensustype = "C"
elif info['CONSENSUS_TYPE'] == "Best replicate":
consensustype = "B"
consensus_base = os.path.join(info[Keys.WORKDIR], 'consensus')
consensus = consensus_base + '.splib'
info['SPLIB'] = consensus
command = "spectrast -L%s -c_RDYDECOY -cI%s -cP%s %s -cN%s %s && " \
"spectrast -L%s -c_BIN! -cA%s -cN%s %s" % (
info['SPLOG'], info['MS_TYPE'], info['IPROB'], rtcorrect, rtcalib_base, peplink,
info['SPLOG'], consensustype, consensus_base, rtcalib)
return info, command
def prepare_run(self, log, info):
if isinstance(info[Keys.PEPXML], list):
raise RuntimeError(
"This ProteinProphet only takes one iProphet inputfile!")
info['IPROB'], info['FDR'] = get_iprob_for_fdr(
info['FDR_CUTOFF'],
info['FDR_TYPE'],
mayuout=info.get('MAYUOUT'),
pepxml=info[Keys.PEPXML])
info['PROTEINPROPHET'] = 'IPROPHET MINPROB%s' % info['IPROB']
wd = info[Keys.WORKDIR]
info['PROTXML'] = os.path.join(wd, 'ProteinProphet.prot.xml')
exe = info.get(Keys.EXECUTABLE, 'ProteinProphet')
command = '%s %s %s %s' % (exe, info[Keys.PEPXML], info['PROTXML'],
info['PROTEINPROPHET'])
return info, command
