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())