Skip to content

Commit

Permalink
first letter of all description set to uppercase
Browse files Browse the repository at this point in the history
  • Loading branch information
@valearna
valearna committed Feb 1, 2019
1 parent 365dd9c commit ad33d67
Showing 1 changed file with 29 additions and 0 deletions.
29 changes: 29 additions & 0 deletions genedescriptions/gene_description.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -94,66 +94,95 @@ def set_or_extend_module_description_and_final_stats(self, module: Module,
self.description = self.gene_name + " " + desc + "." if self.add_gene_name else desc + "."
if module == Module.GO_FUNCTION:
self.go_function_description = self._get_description(desc, self.go_function_description)
self.go_function_description = self.go_function_description[0].upper() + self.go_function_description[1:]
self.stats.set_final_go_ids_f = self._get_merged_ids(module_sentences.get_ids(experimental_only=False),
self.stats.set_final_go_ids_f)
self.stats.set_final_experimental_go_ids_f = self._get_merged_ids(module_sentences.get_ids(
experimental_only=True), self.stats.set_final_experimental_go_ids_f)
elif module == Module.GO_PROCESS:
self.go_process_description = self._get_description(desc, self.go_process_description)
self.go_process_description = self.go_process_description[0].upper() + self.go_process_description[1:]
self.stats.set_final_go_ids_p = self._get_merged_ids(module_sentences.get_ids(experimental_only=False),
self.stats.set_final_go_ids_p)
self.stats.set_final_experimental_go_ids_p = self._get_merged_ids(module_sentences.get_ids(
experimental_only=True), self.stats.set_final_experimental_go_ids_p)
elif module == Module.GO_COMPONENT:
self.go_component_description = self._get_description(desc, self.go_component_description)
self.go_component_description = self.go_component_description[0].upper() + \
self.go_component_description[1:]
self.stats.set_final_go_ids_c = self._get_merged_ids(module_sentences.get_ids(experimental_only=False),
self.stats.set_final_go_ids_c)
self.stats.set_final_experimental_go_ids_c = self._get_merged_ids(module_sentences.get_ids(
experimental_only=True), self.stats.set_final_experimental_go_ids_c)
elif module == Module.EXPRESSION:
self.tissue_expression_description = self._get_description(desc, self.tissue_expression_description)
self.tissue_expression_description = self.tissue_expression_description[0].upper() + \
self.tissue_expression_description[1:]
self.stats.set_final_expression_ids = self._get_merged_ids(
module_sentences.get_ids(experimental_only=False), self.stats.set_final_expression_ids)
self.stats.set_final_experimental_go_ids_c = self._get_merged_ids(module_sentences.get_ids(
experimental_only=True), self.stats.set_final_experimental_go_ids_c)
elif module == Module.EXPRESSION_CLUSTER_GENE:
self.gene_expression_cluster_description = self._get_description(
desc, self.gene_expression_cluster_description)
self.gene_expression_cluster_description = self.gene_expression_cluster_description[0].upper() + \
self.gene_expression_cluster_description[1:]
elif module == Module.EXPRESSION_CLUSTER_ANATOMY:
self.anatomy_expression_cluster_description = self._get_description(
desc, self.anatomy_expression_cluster_description)
self.anatomy_expression_cluster_description = self.anatomy_expression_cluster_description[0].upper() + \
self.anatomy_expression_cluster_description[1:]
elif module == Module.EXPRESSION_CLUSTER_MOLECULE:
self.molecule_expression_cluster_description = self._get_description(
desc, self.molecule_expression_cluster_description)
self.molecule_expression_cluster_description = \
self.molecule_expression_cluster_description[0].upper() + \
self.molecule_expression_cluster_description[1:]
elif module == Module.DO_EXPERIMENTAL:
self.do_experimental_description = self._get_description(desc, self.do_experimental_description)
self.do_experimental_description = self.do_experimental_description[0].upper() + \
self.do_experimental_description[1:]
self.stats.set_final_do_ids = self._get_merged_ids(module_sentences.get_ids(experimental_only=False),
self.stats.set_final_do_ids)
elif module == Module.DO_BIOMARKER:
self.do_biomarker_description = self._get_description(desc, self.do_biomarker_description)
self.do_biomarker_description = self.do_biomarker_description[0].upper() + \
self.do_biomarker_description[1:]
self.stats.set_final_do_ids = self._get_merged_ids(module_sentences.get_ids(experimental_only=False),
self.stats.set_final_do_ids)
elif module == Module.DO_ORTHOLOGY:
self.do_orthology_description = self._get_description(desc, self.do_orthology_description)
self.do_orthology_description = self.do_orthology_description[0].upper() + \
self.do_orthology_description[1:]
self.stats.set_final_do_ids = self._get_merged_ids(module_sentences.get_ids(experimental_only=False),
self.stats.set_final_do_ids)
elif module == Module.SISTER_SP:
self.sister_species_description = self._get_description(desc, self.sister_species_description)
self.sister_species_description = self.sister_species_description[0].upper() + \
self.sister_species_description[1:]
elif module == Module.ORTHOLOGY:
self.orthology_description = self._get_description(desc, self.orthology_description)
self.orthology_description = self.orthology_description[0].upper() + \
self.orthology_description[1:]
elif module == Module.INFO_POOR_HUMAN_FUNCTION:
self.human_gene_function_description = self._get_description(desc, self.human_gene_function_description)
self.human_gene_function_description = self.human_gene_function_description[0].upper() + \
self.human_gene_function_description[1:]
elif module == Module.PROTEIN_DOMAIN:
self.protein_domain_description = self._get_description(desc, self.protein_domain_description)
self.protein_domain_description = self.protein_domain_description[0].upper() + \
self.protein_domain_description[1:]
# Multimodule fields
if module == Module.GO_PROCESS or module == Module.GO_FUNCTION or module == Module.GO_COMPONENT:
self.go_description = "; ".join([sent for sent in [self.go_function_description,
self.go_process_description,
self.go_component_description] if sent])
self.go_description = self.go_description[0].upper() + self.go_description[1:]
if module == Module.DO_EXPERIMENTAL or module == Module.DO_BIOMARKER or module == Module.DO_ORTHOLOGY:
self.do_description = "; ".join([sent for sent in [self.do_experimental_description,
self.do_biomarker_description,
self.do_orthology_description] if sent])
self.do_description = self.do_description[0].upper() + self.do_description[1:]
self.stats.number_final_do_term_covering_multiple_initial_do_terms = self.do_description.count(
"(multiple)")

Expand Down

0 comments on commit ad33d67

Please sign in to comment.