def main(args):
'''
Main function
'''
# check parameters
# extract params for the methods
params = {}
methods = ["sanxot1"]
for method in methods:
if not method in args.params:
_print_exception(
2, "checking the parameters for the {} method".format(method))
match = re.search(r'{\s*' + method + r'\s*:\s*([^\}]*)}', args.params,
re.IGNORECASE)
if match.group():
params[method] = match.group(1)
else:
_print_exception(
2, "checking the parameters for the {} method".format(method))
# get directory from input files
outdir = os.path.dirname(os.path.realpath(args.profile))
# create builder ---
logging.info("create workflow builder")
w = wf.builder(outdir, logging)
logging.info("execute sanxot")
w.sanxot({
"-a": "q2a_outs",
"-d": args.profile,
}, params["sanxot1"])
def main(args):
'''
Main function
'''
# check parameters
# extract params for the methods
params = {}
methods = ["sanxot1"]
for method in methods:
if not method in args.params:
_print_exception( 2, "checking the parameters for the {} method".format(method) )
match = re.search(r'{\s*' + method + r'\s*:\s*([^\}]*)}', args.params, re.IGNORECASE)
if match.group():
params[method] = match.group(1)
else:
_print_exception( 2, "checking the parameters for the {} method".format(method) )
# extract temporal working directory...
if args.tmpdir:
tmpdir = args.tmpdir
# otherwisae, get directory from input files
else:
tmpdir = os.path.dirname(os.path.realpath(args.catfile))+"/tmp"
# create builder ---
logging.info("create workflow builder")
w = wf.builder(tmpdir, logging)
logging.info("execute sanxot")
w.sanxot({
"-a": "c2a_outs",
"-d": args.catfile,
"-z": args.c2afile
}, params["sanxot1"])
def main(args):
'''
Main function
'''
# check parameters
# extract params for the methods
params = {}
methods = ["aljamia1"]
for method in methods:
if not method in args.params:
_print_exception(
2, "checking the parameters for the {} method".format(method))
match = re.search(r'{\s*' + method + r'\s*:\s*([^\}]*)}', args.params,
re.IGNORECASE)
if match.group():
params[method] = match.group(1)
else:
_print_exception(
2, "checking the parameters for the {} method".format(method))
# get directory from input files
outdir = os.path.dirname(os.path.realpath(args.relfile))
# create builder ---
logging.info("create workflow builder")
w = wf.builder(outdir, logging)
logging.info("aljamia for peptide to protein")
w.aljamia({"-x": args.idqfile, "-o": args.relfile}, params["aljamia1"])
def main(args):
'''
Main function
'''
# check parameters
# extract params for the methods
params = {}
methods = ["klibrate1", "sanxot1", "sanxotsieve1", "sanxot2"]
for method in methods:
if not method in args.params:
_print_exception( 2, "checking the parameters for the {} method".format(method) )
match = re.search(r'{\s*' + method + r'\s*:\s*([^\}]*)}', args.params, re.IGNORECASE)
if match.group():
params[method] = match.group(1)
else:
_print_exception( 2, "checking the parameters for the {} method".format(method) )
# extract temporal working directory...
if args.tmpdir:
tmpdir = args.tmpdir
# otherwisae, get directory from input files
else:
tmpdir = os.path.dirname(os.path.realpath(args.relfile))+"/tmp"
# create builder ---
logging.info("create workflow builder")
w = wf.builder(tmpdir, logging)
logging.info("klibrate scans")
w.klibrate({
"-d": args.uscanfile,
"-r": args.relfile,
"-o": args.scanfile
}, params["klibrate1"])
logging.info("execute sanxot")
w.sanxot({
"-a": "s2p_outs",
"-d": args.scanfile,
"-r": args.relfile
}, params["sanxot1"])
logging.info("execute sanxotsieve")
p = { "-d": args.scanfile, "-r": args.relfile, "-f": args.fdr }
if args.variance: # force the variance
p["-v"] = args.variance
else: # use the file variance
p["-V"] = "s2p_outs_infoFile.txt"
w.sanxotsieve(p, params["sanxotsieve1"])
logging.info("execute sanxot")
tagfile = os.path.splitext( os.path.basename(args.scanfile) )[0] + "_tagged.tsv"
p = { "-a": "s2p_nouts", "-d": args.scanfile, "-r": tagfile, "-o": args.pepfile }
if args.variance:
p["-v"] = args.variance
else:
p["-V"] = "s2p_outs_infoFile.txt"
w.sanxot(p, params["sanxot2"])
def main(args):
'''
Main function
'''
# check parameters
# extract params for the methods
params = {}
methods = ["sanxot1", "sanxotsieve1", "sanxot2"]
for method in methods:
if not method in args.params:
_print_exception(
2, "checking the parameters for the {} method".format(method))
match = re.search(r'{\s*' + method + r'\s*:\s*([^\}]*)}', args.params,
re.IGNORECASE)
if match.group():
params[method] = match.group(1)
else:
_print_exception(
2, "checking the parameters for the {} method".format(method))
# get directory from input files
outdir = os.path.dirname(os.path.realpath(args.catfile))
# create builder ---
logging.info("create workflow builder")
w = wf.builder(outdir, logging)
logging.info("execute sanxot")
w.sanxot({
"-a": "q2c_outs",
"-d": args.profile,
"-r": args.relfile
}, params["sanxot1"])
logging.info("execute sanxotsieve")
w.sanxotsieve(
{
"-d": args.profile,
"-r": args.relfile,
"-f": args.fdr,
"-V": "q2c_outs_infoFile.txt"
}, params["sanxotsieve1"])
logging.info("execute sanxot")
tagfile = os.path.splitext(os.path.basename(
args.profile))[0] + "_tagged.xls"
w.sanxot(
{
"-a": "q2c_nouts",
"-d": args.profile,
"-r": tagfile,
"-o": args.catfile,
"-V": "q2c_outs_infoFile.txt",
}, params["sanxot2"])
def main(args):
'''
Main function
'''
# check parameters
# extract params for the methods
params = {}
methods = ["aljamia1"]
for method in methods:
if not method in args.params:
_print_exception(
2, "checking the parameters for the {} method".format(method))
match = re.search(r'{\s*' + method + r'\s*:\s*([^\}]*)}', args.params,
re.IGNORECASE)
if match.group():
params[method] = match.group(1)
else:
_print_exception(
2, "checking the parameters for the {} method".format(method))
# get directory from input files
outdir = os.path.dirname(os.path.realpath(args.relfile))
# create builder ---
logging.info("create workflow builder")
w = wf.builder(outdir, logging)
logging.info("aljamia for peptide to protein")
w.aljamia({
"-x": args.idqfile,
"-o": "p2q_rels_aux.xls"
}, params["aljamia1"])
logging.info('create corrector object')
co = corrector(w.tmpdir + "/p2q_rels_aux.xls", args.species, args.pretxt,
args.indb)
logging.info('calculate the unique protein')
co.get_unique_protein()
logging.info('print output')
co.to_csv(args.relfile)
def main(args):
'''
Main function
'''
# check parameters
# extract params for the methods
params = {}
methods = ["aljamia1", "aljamia2"]
for method in methods:
if not method in args.params:
_print_exception( 2, "checking the parameters for the {} method".format(method) )
match = re.search(r'{\s*' + method + r'\s*:\s*([^\}]*)}', args.params, re.IGNORECASE)
if match.group():
params[method] = match.group(1)
else:
_print_exception( 2, "checking the parameters for the {} method".format(method) )
# extract temporal working directory...
if args.tmpdir:
tmpdir = args.tmpdir
# otherwisae, get directory from input files
else:
tmpdir = os.path.dirname(os.path.realpath(args.relfile))+"/tmp"
# create builder ---
logging.info("create workflow builder")
w = wf.builder(tmpdir, logging)
logging.info("aljamia for scan uncalibrated")
w.aljamia({
"-x": args.idqfile,
"-o": args.scanfile
}, params["aljamia1"])
logging.info("aljamia for s2p relationship")
w.aljamia({
"-x": args.idqfile,
"-o": args.relfile
}, params["aljamia2"])