def prepare_run(self, log, info):
wd = info[Keys.WORKDIR]
basename = os.path.splitext(os.path.split(info[Keys.MZXML])[1])[0]
info[Keys.PEPXML] = os.path.join(wd, basename + ".pepXML") #myrimatch default is pepXML NOT pep.xml
# need to create a working copy to prevent replacement or generic definitions
# with app specific definitions
app_info = info.copy()
app_info['ENZYME'], app_info['MYRIMATCH_MINTERMINICLEAVAGES'] = enzymestr_to_engine(info['ENZYME'],
'Myrimatch')
app_info["STATIC_MODS"], app_info["VARIABLE_MODS"], _ = genmodstr_to_engine(info["STATIC_MODS"],
info["VARIABLE_MODS"], 'Myrimatch')
if app_info['FRAGMASSUNIT'] == 'Da':
app_info['FRAGMASSUNIT'] = 'daltons'
#link DB to cwd
app_info['DBASE'] = os.path.join(wd, os.path.basename(info['DBASE']))
os.symlink(info['DBASE'], app_info['DBASE'])
#tpl = os.path.join(wd, 'myrimatch.cfg')
tpl = 'myrimatch.cfg'
tplfile = os.path.join(wd, tpl)
read_mod_write(app_info, get_tpl_of_class(self), tplfile)
exe_path = app_info['MYRIMATCH_DIR']
exe = app_info['MYRIMATCH_EXE']
command = "{exe} -cpus {threads} -cfg {tpl} -workdir {workdir} -ProteinDatabase {dbase} {mzxml}".format(
exe=os.path.join(exe_path, exe), threads=app_info['THREADS'], tpl=tpl,
workdir=app_info[Keys.WORKDIR], dbase=app_info['DBASE'],
mzxml=app_info[Keys.MZXML])
# update original info object with new keys from working copy
#info = DictUtils.merge(log, info, app_info, priority='left')
return info, command
def prepare_run(self, log, info):
wd = info[Keys.WORKDIR]
exe = info.get(Keys.EXECUTABLE, 'tandem')
# need to create a working copy to prevent replacement with app specific definitions
app_info = info.copy()
app_info = self._define_score(app_info, log)
app_info["STATIC_MODS"], app_info["VARIABLE_MODS"], app_info['TERMINAL_MODS'] = genmodstr_to_engine(info["STATIC_MODS"],
info["VARIABLE_MODS"], 'XTandem')
app_info['ENZYME'], app_info['XTANDEM_SEMI_CLEAVAGE'] = enzymestr_to_engine(info['ENZYME'], 'XTandem')
#files required and written
app_info['XTANDEM_PARAMS'] = os.path.join(wd, 'xtandem.params')
templates.read_mod_write(app_info, templates.get_tpl_of_class(self), app_info['XTANDEM_PARAMS'])
app_info['XTANDEM_INPUT'] = os.path.join(wd, 'xtandem.input')
app_info['XTANDEM_TAXONOMY'] = os.path.join(wd, 'xtandem.taxonomy')
app_info['XTANDEM_RESULT'] = os.path.join(wd, 'xtandem.result')
self._write_input_files(app_info)
#integrated tandem2xml XTANDEM_RESULT conversion
info[Keys.PEPXML] = os.path.join(wd, 'xtandem.pep.xml')
command = '%s %s && Tandem2XML %s %s ' % (
exe, app_info['XTANDEM_INPUT'], app_info['XTANDEM_RESULT'], info[Keys.PEPXML])
return info, command
def _writemail(self, info):
info['USERNAME'] = getpass.getuser()
if info.get('RUNTPP2VIEWER', 'no') == 'no':
info["LINKTEXT"] = "RUNTPP2VIEWER was 'no'. If you want to visualize the results"
else:
basepath = '/IMSB/ra/' + info['USERNAME'] + '/html/petunia/tpp2viewer3_' + info['EXPERIMENT_CODE']
info["LINKTEXT"] = """To visualize the results use:
https://imsb-ra-tpp.ethz.ch/tpp/cgi-bin/PepXMLViewer.cgi?xmlFileName=%s
https://imsb-ra-tpp.ethz.ch/tpp/cgi-bin/protxml2html.pl?xmlfile=%s
In case the links do not work""" % (basepath + '.pep.xml', basepath + '.prot.xml')
info['ENGINES_VERSIONS'] = ''
if 'RUNTANDEM' in info and info['RUNTANDEM'] == 'True':
info['ENGINES_VERSIONS'] += subprocess.check_output("tandem a | grep TANDEM",
shell=True)
if 'RUNOMSSA' in info and info['RUNOMSSA'] == 'True':
info['ENGINES_VERSIONS'] += subprocess.check_output("omssacl -version", shell=True).replace(
"2.1.8", "2.1.9")
if 'RUNMYRIMATCH' in info and info['RUNMYRIMATCH'] == 'True':
info['ENGINES_VERSIONS'] += subprocess.check_output("myrimatch 2>&1 | grep MyriMatch",
shell=True)
if 'RUNCOMET' in info and info['RUNCOMET'] == 'True':
info['ENGINES_VERSIONS'] += subprocess.check_output("comet 2>&1 | grep version", shell=True)
info['ENGINES_VERSIONS'] = info['ENGINES_VERSIONS'].strip()
info['TPPVERSION'] = subprocess.check_output("InteractParser 2>&1 | grep TPP", shell=True).split("(")[1]
templates.read_mod_write(info, templates.get_tpl_of_class(self), info['MAILFILE'])
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):
wd = info[Keys.WORKDIR]
exe = info.get(Keys.EXECUTABLE, 'tandem')
# need to create a working copy to prevent replacement with app specific definitions
app_info = info.copy()
app_info = self._define_score(app_info, log)
app_info["STATIC_MODS"], app_info["VARIABLE_MODS"], app_info[
'TERMINAL_MODS'] = genmodstr_to_engine(info["STATIC_MODS"],
info["VARIABLE_MODS"],
'XTandem')
app_info['ENZYME'], app_info[
'XTANDEM_SEMI_CLEAVAGE'] = enzymestr_to_engine(
info['ENZYME'], 'XTandem')
#files required and written
app_info['XTANDEM_PARAMS'] = os.path.join(wd, 'xtandem.params')
templates.read_mod_write(app_info, templates.get_tpl_of_class(self),
app_info['XTANDEM_PARAMS'])
app_info['XTANDEM_INPUT'] = os.path.join(wd, 'xtandem.input')
app_info['XTANDEM_TAXONOMY'] = os.path.join(wd, 'xtandem.taxonomy')
app_info['XTANDEM_RESULT'] = os.path.join(wd, 'xtandem.result')
self._write_input_files(app_info)
#integrated tandem2xml XTANDEM_RESULT conversion
info[Keys.PEPXML] = os.path.join(wd, 'xtandem.pep.xml')
command = '%s %s && Tandem2XML %s %s ' % (
exe, app_info['XTANDEM_INPUT'], app_info['XTANDEM_RESULT'],
info[Keys.PEPXML])
return info, command
def prepare_run(self, log, info):
wd = info[Keys.WORKDIR]
basename = os.path.join(wd, os.path.splitext(os.path.split(info[Keys.MZXML])[1])[0])
info[Keys.PEPXML] = basename + '.pep.xml'
# need to create a working copy to prevent replacement or generic definitions
# with app specific definitions
app_info = info.copy()
if info['PRECMASSUNIT'] == 'Da':
app_info['PRECMASSUNIT'] = '0'
elif info['PRECMASSUNIT'] == 'ppm':
app_info['PRECMASSUNIT'] = '2'
else:
raise RuntimeError("Precmassunit %s unknown" % info['PRECMASSUNIT'])
if info['FRAGMASSUNIT'] == 'ppm':
raise RuntimeError("Comet does not support frag mass error unit PPM")
if not 0.01 < float(app_info['FRAGMASSERR']) < 1.1:
log.warn('Very high or low fragmasserror ' + app_info['FRAGMASSERR'])
app_info["STATIC_MODS"], app_info["VARIABLE_MODS"], _ = genmodstr_to_engine(info["STATIC_MODS"],
info["VARIABLE_MODS"], 'Comet')
app_info['ENZYME'], app_info['NUM_TERM_CLEAVAGES'] = enzymestr_to_engine(info['ENZYME'], 'Comet')
tplfile = os.path.join(wd, "comet.params")
template = get_tpl_of_class(self)
read_mod_write(app_info,template, tplfile)
exe_path = app_info['COMET_DIR']
exe = app_info['COMET_EXE']
command = "{exe} -N{basename} -P{tplfile} {mzxml}".format(exe=os.path.join(exe_path, exe), basename=basename, tplfile=tplfile, mzxml=info[Keys.MZXML])
return info, command
def prepare_run(self, log, info):
wd = info[Keys.WORKDIR]
#add in blast and mzxml2mgf conversion
omssadbase = os.path.join(wd, os.path.basename(info['DBASE']))
os.symlink(info['DBASE'], omssadbase)
mzxmlbase = os.path.basename(info[Keys.MZXML])
mzxmllink = os.path.join(wd, mzxmlbase)
mgffile = os.path.join(wd, os.path.splitext(mzxmlbase)[0] + '.mgf')
os.symlink(info[Keys.MZXML], mzxmllink)
basename = os.path.splitext(os.path.split(info[Keys.MZXML])[1])[0]
result = os.path.join(wd, basename + '.pep.xml')
iresult = os.path.join(wd, basename + '.withRT.pep.xml')
info[Keys.PEPXML] = iresult
# need to create a working copy to prevent replacement or generic definitions
# with app specific definitions
app_info = info.copy()
app_info['DBASE'] = omssadbase
if info['FRAGMASSUNIT'] == 'ppm':
raise RuntimeError(
"OMSSA does not support frag mass error unit PPM")
app_info['USERMODXML'] = os.path.join(wd, 'usermod.xml')
app_info["STATIC_MODS"], app_info[
"VARIABLE_MODS"], tpl = genmodstr_to_engine(
info["STATIC_MODS"], info["VARIABLE_MODS"], 'Omssa')
if app_info['STATIC_MODS']:
app_info['STATIC_MODS'] = "-mf " + app_info['STATIC_MODS']
if app_info['VARIABLE_MODS']:
app_info['VARIABLE_MODS'] = "-mv " + app_info['VARIABLE_MODS']
open(app_info['USERMODXML'], 'w').write(tpl)
app_info['ENZYME'], _ = enzymestr_to_engine(info['ENZYME'], 'Omssa')
mod_template = templates.modify_template(
app_info,
templates.read_template(templates.get_tpl_of_class(self)))
# necessary check for the precursor mass unig
if app_info['PRECMASSUNIT'].lower() == "ppm":
mod_template += ' -teppm'
log.debug(
'added [ -teppm] to modified template because the precursor mass is defined in ppm'
)
exe = app_info.get(Keys.EXECUTABLE, 'omssacl')
#grep to prevent log overflow, InteractParser to add RT to pepXML
#note: mod_template paths are quoted in the template file
command = 'makeblastdb -dbtype prot -in "%s" && ' \
'MzXML2Search -mgf "%s" | grep -v scan && ' \
'"%s" %s -fm "%s" -op "%s" && ' \
'InteractParser "%s" "%s" -S' % (
omssadbase,
mzxmllink,
exe, mod_template, mgffile, result,
iresult, result)
return info, command
def run(self, log, info):
info = create_workdir(log, info)
info['TEMPLATEFILE'] = os.path.join(info[Keys.WORKDIR], "template_out.tpl")
templates.read_mod_write(info, templates.get_tpl_of_class(self), info['TEMPLATEFILE'])
log.debug("Templatefile sucessfully written. Contents are [%s]" % open(info['TEMPLATEFILE']).read())
return info
def prepare_run(self, log, info):
wd = info[Keys.WORKDIR]
basename = os.path.join(
wd,
os.path.splitext(os.path.split(info[Keys.MZXML])[1])[0])
info[Keys.PEPXML] = basename + '.pep.xml'
# need to create a working copy to prevent replacement or generic definitions
# with app specific definitions
app_info = info.copy()
if info['PRECMASSUNIT'] == 'Da':
app_info['PRECMASSUNIT'] = '0'
elif info['PRECMASSUNIT'] == 'ppm':
app_info['PRECMASSUNIT'] = '2'
else:
raise RuntimeError("Precmassunit %s unknown" %
info['PRECMASSUNIT'])
if info['FRAGMASSUNIT'] == 'ppm':
raise RuntimeError(
"Comet does not support frag mass error unit PPM")
# Note: FRAGMASSERR does not apply to Comet; instead use pre-defined
# FRAGBINTOL and FRAGBINOFF values
frag_bin_tol, frag_bin_off, frag_ions_theor = self.get_fragment_ions_values(
info.get('COMET_FRAGMENT_IONS', None))
app_info.update({
'FRAGBINTOL': frag_bin_tol,
'FRAGBINOFF': frag_bin_off,
'FRAGIONSTHEOR': frag_ions_theor,
})
app_info["STATIC_MODS"], app_info[
"VARIABLE_MODS"], _ = genmodstr_to_engine(info["STATIC_MODS"],
info["VARIABLE_MODS"],
'Comet')
app_info['ENZYME'], app_info[
'NUM_TERM_CLEAVAGES'] = enzymestr_to_engine(
info['ENZYME'], 'Comet')
tplfile = os.path.join(wd, "comet.params")
template = get_tpl_of_class(self)
read_mod_write(app_info, template, tplfile)
exe_path = app_info['COMET_DIR']
exe = app_info['COMET_EXE']
command = "{exe} -N{basename} -P{tplfile} {mzxml}".format(
exe=os.path.join(exe_path, exe),
basename=basename,
tplfile=tplfile,
mzxml=info[Keys.MZXML])
return info, command
def run(self, log, info):
info = create_workdir(log, info)
info['TEMPLATEFILE'] = os.path.join(info[Keys.WORKDIR],
"template_out.tpl")
templates.read_mod_write(info, templates.get_tpl_of_class(self),
info['TEMPLATEFILE'])
log.debug("Templatefile sucessfully written. Contents are [%s]" %
open(info['TEMPLATEFILE']).read())
return info
def prepare_run(self, log, info):
wd = info[Keys.WORKDIR]
#add in blast and mzxml2mgf conversion
omssadbase = os.path.join(wd, os.path.basename(info['DBASE']))
os.symlink(info['DBASE'], omssadbase)
mzxmlbase = os.path.basename(info[Keys.MZXML])
mzxmllink = os.path.join(wd, mzxmlbase)
mgffile = os.path.join(wd, os.path.splitext(mzxmlbase)[0] + '.mgf')
os.symlink(info[Keys.MZXML], mzxmllink)
basename = os.path.splitext(os.path.split(info[Keys.MZXML])[1])[0]
result = os.path.join(wd, basename+'.pep.xml')
iresult = os.path.join(wd, basename+'.withRT.pep.xml')
info[Keys.PEPXML] = iresult
# need to create a working copy to prevent replacement or generic definitions
# with app specific definitions
app_info = info.copy()
app_info['DBASE'] = omssadbase
if info['FRAGMASSUNIT'] == 'ppm':
raise RuntimeError("OMSSA does not support frag mass error unit PPM")
app_info['USERMODXML'] = os.path.join(wd, 'usermod.xml')
app_info["STATIC_MODS"], app_info["VARIABLE_MODS"], tpl = genmodstr_to_engine(info["STATIC_MODS"],
info["VARIABLE_MODS"], 'Omssa')
if app_info['STATIC_MODS']:
app_info['STATIC_MODS'] = "-mf " + app_info['STATIC_MODS']
if app_info['VARIABLE_MODS']:
app_info['VARIABLE_MODS'] = "-mv " + app_info['VARIABLE_MODS']
open(app_info['USERMODXML'], 'w').write(tpl)
app_info['ENZYME'], _ = enzymestr_to_engine(info['ENZYME'], 'Omssa')
mod_template = templates.modify_template(app_info, templates.read_template(templates.get_tpl_of_class(self)))
# necessary check for the precursor mass unig
if app_info['PRECMASSUNIT'].lower() == "ppm":
mod_template += ' -teppm'
log.debug('added [ -teppm] to modified template because the precursor mass is defined in ppm')
exe = app_info.get(Keys.EXECUTABLE, 'omssacl')
#grep to prevent log overflow, InteractParser to add RT to pepXML
#note: mod_template paths are quoted in the template file
command = 'makeblastdb -dbtype prot -in "%s" && ' \
'MzXML2Search -mgf "%s" | grep -v scan && ' \
'"%s" %s -fm "%s" -op "%s" && ' \
'InteractParser "%s" "%s" -S' % (
omssadbase,
mzxmllink,
exe, mod_template, mgffile, result,
iresult, result)
return info, command
def prepare_run(self, log, info):
for f in info['DSSOUT']:
if "dataset.properties" in f:
dsprop = ConfigObj(f)
info["SEQ"] = dsprop["SEQ"]
info["IN__FILE__ALIGNMENT"] = os.path.join(info["ROSETTA_EXTRACTDIR"], dsprop["ALIGNMENT_FILE"])
info["IN__FILE__FASTA"] = os.path.join(info["ROSETTA_EXTRACTDIR"], dsprop["FILE_STEM"] + ".fasta")
info["FRAG3"] = os.path.join(info["ROSETTA_EXTRACTDIR"], dsprop["3MERS"])
info["FRAG9"] = os.path.join(info["ROSETTA_EXTRACTDIR"], dsprop["9MERS"])
info["LOOPS__FRAG_SIZES"] = "9 3 1"
info["LOOPS__FRAG_FILES"] = info["FRAG9"] + " " + info["FRAG3"] + " none"
info["IN__FILE__PSIPRED_SS2"] = os.path.join(info["ROSETTA_EXTRACTDIR"], dsprop["FILE_STEM"] + ".psipred_ss2")
info['ROSETTA_OUT'] = os.path.join(info[Keys.WORKDIR], 'default.out')
#needed because of rosetta && gzip
info['ROSETTA_COMPRESSEDOUT'] = info['ROSETTA_OUT'] + '.gz'
info["IN__FILE__TEMPLATE_PDB"] = ""
for pdb in dsprop["TEMPLATES"].split():
info["IN__FILE__TEMPLATE_PDB"] += os.path.join(info["ROSETTA_EXTRACTDIR"], pdb) + " "
info["IN__FILE__TEMPLATE_PDB"] = info["IN__FILE__TEMPLATE_PDB"].strip()
info["DATABASE"] = os.environ["ROSETTA3_DB"]
info["ROSETTA_VERSION"] = subprocess.check_output("which %s | cut -d/ -f5" % info[Keys.EXECUTABLE],
shell=True).strip()
info["INFRASTRUCTURE"] = "BRUTUS"
#change the on/off flags only in the template, not the info
app_info = info.copy()
app_info['RUN__SHUFFLE'] = "-run:shuffle" if info['RUN__SHUFFLE'] == "TRUE" else ""
app_info['IN__FILE__FULLATOM'] = "-in:file:fullatom" if info['IN__FILE__FULLATOM'] == "TRUE" else ""
app_info['IDEALIZE_AFTER_LOOP_CLOSE'] = "-idealize_after_loop_close" if info[
'IDEALIZE_AFTER_LOOP_CLOSE'] == "TRUE" else ""
app_info['LOOPS__EXTENDED'] = "-loops:extended" if info['LOOPS__EXTENDED'] == "TRUE" else ""
app_info['LOOPS__BUILD_INITIAL'] = "-loops:build_initial" if info['LOOPS__BUILD_INITIAL'] == "TRUE" else ""
app_info['RELAX__FAST'] = "-relax:fast" if info['RELAX__FAST'] == "TRUE" else ""
app_info['SILENT_DECOYTIME'] = "-silent_decoytime" if info['SILENT_DECOYTIME'] == "TRUE" else ""
app_info['BGDT'] = "-bGDT" if info['BGDT'] == "TRUE" else ""
app_info['EVALUATION__GDTMM'] = "-evaluation:gdtmm" if info['EVALUATION__GDTMM'] == "TRUE" else ""
tpl = os.path.join(info[Keys.WORKDIR], "flags")
templates.read_mod_write(app_info, templates.get_tpl_of_class(self), tpl)
command = "%s @%s && gzip %s" % (app_info[Keys.EXECUTABLE], tpl, app_info['ROSETTA_OUT'])
return info, command
def prepare_run(self, log, info):
wd = info[Keys.WORKDIR]
basename = os.path.join(wd, os.path.splitext(os.path.split(info[Keys.MZXML])[1])[0])
info[Keys.PEPXML] = basename + '.pep.xml'
# need to create a working copy to prevent replacement or generic definitions
# with app specific definitions
app_info = info.copy()
if info['PRECMASSUNIT'] == 'Da':
app_info['PRECMASSUNIT'] = '0'
elif info['PRECMASSUNIT'] == 'ppm':
app_info['PRECMASSUNIT'] = '2'
else:
raise RuntimeError("Precmassunit %s unknown" % info['PRECMASSUNIT'])
if info['FRAGMASSUNIT'] == 'ppm':
raise RuntimeError("Comet does not support frag mass error unit PPM")
# Note: FRAGMASSERR does not apply to Comet; instead use pre-defined
# FRAGBINTOL and FRAGBINOFF values
frag_bin_tol, frag_bin_off, frag_ions_theor = self.get_fragment_ions_values(
info.get('COMET_FRAGMENT_IONS', None))
app_info.update({
'FRAGBINTOL': frag_bin_tol,
'FRAGBINOFF': frag_bin_off,
'FRAGIONSTHEOR': frag_ions_theor,
})
app_info["STATIC_MODS"], app_info["VARIABLE_MODS"], _ = genmodstr_to_engine(info["STATIC_MODS"],
info["VARIABLE_MODS"], 'Comet')
app_info['ENZYME'], app_info['NUM_TERM_CLEAVAGES'] = enzymestr_to_engine(info['ENZYME'], 'Comet')
tplfile = os.path.join(wd, "comet.params")
template = get_tpl_of_class(self)
read_mod_write(app_info,template, tplfile)
exe_path = app_info['COMET_DIR']
exe = app_info['COMET_EXE']
command = "{exe} -N{basename} -P{tplfile} {mzxml}".format(exe=os.path.join(exe_path, exe), basename=basename, tplfile=tplfile, mzxml=info[Keys.MZXML])
return info, command
def prepare_run(self, log, info):
wd = info[Keys.WORKDIR]
#required because openbis requires prot.xml and openms protXML
protlink = os.path.join(wd, 'protein.protXML')
os.symlink(info['PROTXML'], protlink)
info['PROTXML'] = protlink
#copy info to not destroy original
app_info = info.copy()
app_info['FEATUREXMLLIST'] = ''
if not isinstance(app_info['FEATUREXML'], list):
raise RuntimeError(
"Cannot perform LFQ with only one featurexml/sample!")
for i in app_info['FEATUREXML']:
app_info['FEATUREXMLLIST'] += '<LISTITEM value="' + i + '"/>'
tpl = os.path.join(wd, 'part2_ma_fl.toppas')
templates.read_mod_write(app_info, templates.get_tpl_of_class(self),
tpl)
#add toppas file path, will be added in dropbox
info["TOPPASFILES"].append(tpl)
rawprot = os.path.join(wd, 'TOPPAS_out/009-ProteinQuantifier/*.csv')
rawpep = os.path.join(wd, 'TOPPAS_out/010-ProteinQuantifier/*.csv')
rawconsensusxml = os.path.join(
wd, 'TOPPAS_out/011-FeatureLinker*/*.consensusXML')
info['PROTCSV'] = os.path.join(wd, 'proteins.csv')
info['PEPCSV'] = os.path.join(wd, 'peptides.csv')
info['CONSENSUSXML'] = os.path.join(wd, 'FeatureLinker.consensusXML')
command = 'ExecutePipeline -in %s -out_dir %s && chmod -R g+w %s && ' \
'mv -v %s %s && ' \
'mv -v %s %s && ' \
'mv -v %s %s' % (
tpl, wd, wd,
rawprot, info['PROTCSV'],
rawpep, info['PEPCSV'],
rawconsensusxml, info['CONSENSUSXML'])
return info, command
def _writemail(self, info):
info['USERNAME'] = getpass.getuser()
if info.get('RUNTPP2VIEWER', 'no') == 'no':
info[
"LINKTEXT"] = "RUNTPP2VIEWER was 'no'. If you want to visualize the results"
else:
# basepath = '/IMSB/ra/' + info['USERNAME'] + '/html/petunia/tpp2viewer3_' + info['EXPERIMENT_CODE']
basepath = '/nfs/195.176.109.15/nas/fs2102/biol_ibt_usr_s1/' + info[
'USERNAME'] + '/html/petunia/tpp2viewer3_' + info[
'EXPERIMENT_CODE']
info["LINKTEXT"] = """To visualize the results use:
https://imsb-ra-tpp.ethz.ch/tpp/cgi-bin/PepXMLViewer.cgi?xmlFileName=%s
https://imsb-ra-tpp.ethz.ch/tpp/cgi-bin/protxml2html.pl?xmlfile=%s
In case the links do not work""" % (basepath + '.pep.xml',
basepath + '.prot.xml')
info['ENGINES_VERSIONS'] = ''
if 'RUNTANDEM' in info and info['RUNTANDEM'] == 'True':
info['ENGINES_VERSIONS'] += subprocess.check_output(
"tandem a | grep TANDEM", shell=True)
if 'RUNOMSSA' in info and info['RUNOMSSA'] == 'True':
info['ENGINES_VERSIONS'] += subprocess.check_output(
"omssacl -version", shell=True).replace("2.1.8", "2.1.9")
if 'RUNMYRIMATCH' in info and info['RUNMYRIMATCH'] == 'True':
info['ENGINES_VERSIONS'] += subprocess.check_output(
"myrimatch 2>&1 | grep MyriMatch", shell=True)
if 'RUNCOMET' in info and info['RUNCOMET'] == 'True':
info['ENGINES_VERSIONS'] += subprocess.check_output(
"comet 2>&1 | grep version", shell=True)
info['ENGINES_VERSIONS'] = info['ENGINES_VERSIONS'].strip()
info['TPPVERSION'] = subprocess.check_output(
"InteractParser 2>&1 | grep TPP", shell=True).split("(")[1]
templates.read_mod_write(info, templates.get_tpl_of_class(self),
info['MAILFILE'])
def prepare_run(self, log, info):
wd = info[Keys.WORKDIR]
#required because openbis requires prot.xml and openms protXML
protlink = os.path.join(wd, 'protein.protXML')
os.symlink(info['PROTXML'], protlink)
info['PROTXML'] = protlink
#copy info to not destroy original
app_info = info.copy()
app_info['FEATUREXMLLIST'] = ''
if not isinstance(app_info['FEATUREXML'],list):
raise RuntimeError("Cannot perform LFQ with only one featurexml/sample!")
for i in app_info['FEATUREXML']:
app_info['FEATUREXMLLIST'] += '<LISTITEM value="' + i + '"/>'
tpl = os.path.join(wd, 'part2_ma_fl.toppas')
templates.read_mod_write(app_info, templates.get_tpl_of_class(self), tpl)
#add toppas file path, will be added in dropbox
info["TOPPASFILES"].append(tpl)
rawprot = os.path.join(wd, 'TOPPAS_out/009-ProteinQuantifier/*.csv')
rawpep = os.path.join(wd, 'TOPPAS_out/010-ProteinQuantifier/*.csv')
rawconsensusxml = os.path.join(wd, 'TOPPAS_out/011-FeatureLinker*/*.consensusXML')
info['PROTCSV'] = os.path.join(wd, 'proteins.csv')
info['PEPCSV'] = os.path.join(wd, 'peptides.csv')
info['CONSENSUSXML'] = os.path.join(wd, 'FeatureLinker.consensusXML')
command = 'ExecutePipeline -in %s -out_dir %s && chmod -R g+w %s && ' \
'mv -v %s %s && ' \
'mv -v %s %s && ' \
'mv -v %s %s' % (
tpl, wd, wd,
rawprot, info['PROTCSV'],
rawpep, info['PEPCSV'],
rawconsensusxml, info['CONSENSUSXML'])
return info, command
def prepare_run(self, log, info):
for f in info['DSSOUT']:
if "dataset.properties" in f:
dsprop = ConfigObj(f)
info["SEQ"] = dsprop["SEQ"]
info["IN__FILE__ALIGNMENT"] = os.path.join(info["ROSETTA_EXTRACTDIR"],
dsprop["ALIGNMENT_FILE"])
info["IN__FILE__FASTA"] = os.path.join(info["ROSETTA_EXTRACTDIR"],
dsprop["FILE_STEM"] + ".fasta")
info["FRAG3"] = os.path.join(info["ROSETTA_EXTRACTDIR"],
dsprop["3MERS"])
info["FRAG9"] = os.path.join(info["ROSETTA_EXTRACTDIR"],
dsprop["9MERS"])
info["LOOPS__FRAG_SIZES"] = "9 3 1"
info["LOOPS__FRAG_FILES"] = info["FRAG9"] + " " + info[
"FRAG3"] + " none"
info["IN__FILE__PSIPRED_SS2"] = os.path.join(
info["ROSETTA_EXTRACTDIR"], dsprop["FILE_STEM"] + ".psipred_ss2")
info['ROSETTA_OUT'] = os.path.join(info[Keys.WORKDIR], 'default.out')
#needed because of rosetta && gzip
info['ROSETTA_COMPRESSEDOUT'] = info['ROSETTA_OUT'] + '.gz'
info["IN__FILE__TEMPLATE_PDB"] = ""
for pdb in dsprop["TEMPLATES"].split():
info["IN__FILE__TEMPLATE_PDB"] += os.path.join(
info["ROSETTA_EXTRACTDIR"], pdb) + " "
info["IN__FILE__TEMPLATE_PDB"] = info["IN__FILE__TEMPLATE_PDB"].strip()
info["DATABASE"] = os.environ["ROSETTA3_DB"]
info["ROSETTA_VERSION"] = subprocess.check_output(
"which %s | cut -d/ -f5" % info[Keys.EXECUTABLE],
shell=True).strip()
info["INFRASTRUCTURE"] = "BRUTUS"
#change the on/off flags only in the template, not the info
app_info = info.copy()
app_info['RUN__SHUFFLE'] = "-run:shuffle" if info[
'RUN__SHUFFLE'] == "TRUE" else ""
app_info['IN__FILE__FULLATOM'] = "-in:file:fullatom" if info[
'IN__FILE__FULLATOM'] == "TRUE" else ""
app_info[
'IDEALIZE_AFTER_LOOP_CLOSE'] = "-idealize_after_loop_close" if info[
'IDEALIZE_AFTER_LOOP_CLOSE'] == "TRUE" else ""
app_info['LOOPS__EXTENDED'] = "-loops:extended" if info[
'LOOPS__EXTENDED'] == "TRUE" else ""
app_info['LOOPS__BUILD_INITIAL'] = "-loops:build_initial" if info[
'LOOPS__BUILD_INITIAL'] == "TRUE" else ""
app_info['RELAX__FAST'] = "-relax:fast" if info[
'RELAX__FAST'] == "TRUE" else ""
app_info['SILENT_DECOYTIME'] = "-silent_decoytime" if info[
'SILENT_DECOYTIME'] == "TRUE" else ""
app_info['BGDT'] = "-bGDT" if info['BGDT'] == "TRUE" else ""
app_info['EVALUATION__GDTMM'] = "-evaluation:gdtmm" if info[
'EVALUATION__GDTMM'] == "TRUE" else ""
tpl = os.path.join(info[Keys.WORKDIR], "flags")
templates.read_mod_write(app_info, templates.get_tpl_of_class(self),
tpl)
command = "%s @%s && gzip %s" % (app_info[Keys.EXECUTABLE], tpl,
app_info['ROSETTA_OUT'])
return info, command
