def run_real(self):
"""Runs the applications"""
if len(self.args) != 3:
self.error("exactly three input files are expected" + str(len(self.args)))
if self.options.ev_codes not in self.evidence:
self.error("The three valid types of evidence codes are: " +
"EXP, ALL_BUT_IEA, and ALL")
self.options.results_by_protein = self.__parse_bool(self.options.results_by_protein)
if not self.options.results_by_protein and not self.options.results_by_arch:
self.error("Either results by protein or by arch should be set")
if self.options.max_pvalue < 0.0 or self.options.max_pvalue > 1.0:
self.error("The maximum p-value should be between 0.0 and 1.0")
codes = set(self.evidence[self.options.ev_codes])
go_file, archA, goaB = self.args
self.log.info("Loading GO tree from %s..." % go_file)
self.go_tree = GOTree.from_obo(go_file)
goa = self.read_goa_file(goaB, codes)
if not self.options.source_arch and self.options.both:
self.error("A source architecture file should be specified in 'both' mode")
if not self.options.source_arch:
self._transfer_from_same_file(goa, archA)
elif not self.options.both:
self._transfer_from_other_file(goa, archA, self.options.source_arch)
else:
self._transfer_from_both(goa, archA, self.options.source_arch)
def run_real(self):
"""Runs the overrepresentation analysis application"""
if len(self.args) != 3:
self.error("expected exactly three input file names")
go_tree_file, go_mapping_file, input_file = self.args
self.log.info("Loading GO tree from %s..." % go_tree_file)
self.go_tree = GOTree.from_obo(go_tree_file)
self.log.info("Loading InterPro --> GO mapping from %s..." % \
go_mapping_file)
self.go_mapping = InterPro2GOMapping.from_file(go_mapping_file, self.go_tree)
self.log.info("Processing domain architectures from %s..." % \
input_file)
return self.process_file(input_file)
def run_real(self):
"""Runs the label assignment application"""
if len(self.args) != 3:
self.error("expected exactly three input file names")
go_tree_file, go_mapping_file, input_file = self.args
self.log.info("Loading GO tree from %s...", go_tree_file)
self.go_tree = GOTree.from_obo(go_tree_file)
self.log.info("Loading InterPro --> GO mapping from %s...",
go_mapping_file)
self.go_mapping = InterPro2GOMapping.from_file(go_mapping_file,
self.go_tree)
self.log.info("Processing domain architectures from %s...", input_file)
return self.process_file(input_file)
def run_real(self):
"""Runs the overrepresentation analysis application"""
if len(self.args) != 3:
self.error("expected exactly three input file names")
go_tree_file, go_mapping_file, input_file = self.args
self.options.results_by_protein = self.__parse_bool(self.options.results_by_protein)
if not self.options.results_by_protein and not self.options.arch_file:
self.error("Either results by protein or by arch should be set")
self.log.info("Loading GO tree from %s..." % go_tree_file)
self.go_tree = GOTree.from_obo(go_tree_file)
self.log.info("Loading InterPro --> GO mapping from %s..." % \
go_mapping_file)
self.go_mapping = InterPro2GOMapping.from_file(go_mapping_file, self.go_tree)
self.log.info("Processing domain architectures from %s..." % \
input_file)
return self.process_file(input_file)
def run_real(self):
"""Runs the overrepresentation analysis application"""
if len(self.args) != 3:
self.error("expected exactly three input file names")
go_tree_file, go_mapping_file, input_file = self.args
rbp = self.options.results_by_protein
self.options.results_by_protein = self.__parse_bool(rbp)
if not self.options.results_by_protein and not self.options.arch_file:
self.error("Either results by protein or by arch should be set")
self.log.info("Loading GO tree from %s...", go_tree_file)
self.go_tree = GOTree.from_obo(go_tree_file)
self.log.info("Loading InterPro --> GO mapping from %s...",
go_mapping_file)
self.go_mapping = InterPro2GOMapping.from_file(go_mapping_file,
self.go_tree)
self.log.info("Processing domain architectures from %s...", input_file)
return self.process_file(input_file)
def run_real(self):
"""Runs the applications"""
if len(self.args) != 3:
self.error("exactly three input files are expected" +
str(len(self.args)))
if self.options.ev_codes not in self.evidence:
self.error("The three valid types of evidence codes are: " +
"EXP, ALL_BUT_IEA, and ALL")
rbp = self.options.results_by_protein
self.options.results_by_protein = self.__parse_bool(rbp)
if not self.options.results_by_protein\
and not self.options.results_by_arch:
self.error("Either results by protein or by arch should be set")
if self.options.max_pvalue < 0.0 or self.options.max_pvalue > 1.0:
self.error("The maximum p-value should be between 0.0 and 1.0")
codes = set(self.evidence[self.options.ev_codes])
go_file, arch_a, goa_b = self.args
self.log.info("Loading GO tree from %s...", go_file)
self.go_tree = GOTree.from_obo(go_file)
goa = self.read_goa_file(goa_b, codes)
if not self.options.source_arch and self.options.both:
self.error("A source architecture file "
"should be specified in 'both' mode")
if not self.options.source_arch:
self._transfer_from_same_file(goa, arch_a)
elif not self.options.both:
self._transfer_from_other_file(goa, arch_a,
self.options.source_arch)
else:
self._transfer_from_both(goa, arch_a, self.options.source_arch)
def __init__(self, go_file, goa_file, output_directory, proteins):
self.go_tree = GOTree.from_obo(go_file)
self.terms_per_ontology = defaultdict(set)
self.ontology_per_term = {}
for goterm, term in self.go_tree.terms.items():
try:
namespace = str(term.tags["namespace"][0])
goterm_id = str(term.tags["id"][0])
self.terms_per_ontology[namespace].add(goterm_id)
self.ontology_per_term[goterm_id] = namespace
except KeyError:
# this is done to avoid reading the Typedef entries
pass
for ontology, terms in self.terms_per_ontology.items():
print ontology, " ", len(terms)
self.goa = self._read_goa_file(goa_file)
self.output_dir = output_directory
self._create_output_directory()
self.proteins = set()
with open(proteins, "r") as fin:
for line in fin:
self.proteins.add(line.strip())
def __init__(self, go_file, goa_file, output_directory, proteins):
self.go_tree = GOTree.from_obo(go_file)
self.terms_per_ontology = defaultdict(set)
self.ontology_per_term = {}
for _goterm, term in self.go_tree.terms.items():
try:
namespace = str(term.tags["namespace"][0])
goterm_id = str(term.tags["id"][0])
self.terms_per_ontology[namespace].add(goterm_id)
self.ontology_per_term[goterm_id] = namespace
except KeyError:
# this is done to avoid reading the Typedef entries
pass
for ontology, terms in self.terms_per_ontology.items():
print("{} {}".format(ontology, len(terms)))
self.goa = self._read_goa_file(goa_file)
self.output_dir = output_directory
self._create_output_directory()
self.proteins = set()
with open(proteins, "r") as fin:
for line in fin:
self.proteins.add(line.strip())