def test_mod(self):
static, var, _ = genmodstr_to_engine("Carbamidomethyl (C);; Biotin(K) ;",
"300/300.1 (STY);Label:13C(6)15N(4) (H)",
"Myrimatch")
print static, var
self.assertEqual(static,"C 57.021464 K 226.077598")
self.assertEqual(var,"[STY] * 300.000000 [H] * 10.008269")
with self.assertRaises(Exception):
genmodstr_to_engine("Doesnotexist (C)", "", "Myrimatch")
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.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]
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 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]
#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):
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
class Test(unittest.TestCase):
def test_mod(self):
static, var, _ = genmodstr_to_engine("Carbamidomethyl (C);; Biotin(K) ;",
"300/300.1 (STY);Label:13C(6)15N(4) (H)",
"Myrimatch")
print static, var
self.assertEqual(static,"C 57.021464 K 226.077598")
self.assertEqual(var,"[STY] * 300.000000 [H] * 10.008269")
with self.assertRaises(Exception):
genmodstr_to_engine("Doesnotexist (C)", "", "Myrimatch")
if __name__ == "__main__":
if len(sys.argv) > 1 and 'test' not in sys.argv[1]:
mod = sys.argv[1]
print "Testing modification '%s'" % mod
try:
for i in ['XTandem', 'Omssa', 'Myrimatch', 'Comet']:
genmodstr_to_engine("", mod, i)
# print out one example to show masses. myri varmod is most compact
_, p, _ = genmodstr_to_engine("", mod, 'Comet')
print p,_
print "OK"
except Exception, e:
raise
print "ERROR"
print e.message
else:
unittest.main()
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