diff --git a/gga_init.py b/gga_init.py index 5eb6f249c4f9e27ee813041d1b2afa1279c9d1b0..e91ea41dd11e877a7116cb1b8e95269065e60021 100755 --- a/gga_init.py +++ b/gga_init.py @@ -128,8 +128,8 @@ class DeploySpeciesStack(speciesData.SpeciesData): input_vars = {"genus": self.genus_lowercase, "Genus": self.genus_uppercase, "species": self.species, "genus_species": self.genus_species, "genus_species_strain_sex": self.species_folder_name, - "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species_lower, self.sex), - "strain": self.strain, "sex": self.sex, "Genus_species": "{0} {1}".format(self.genus_uppercase, self.species_lower), + "genus_species_sex": "{0}_{1}_{2}".format(self.genus_lowercase, self.species_lowercase, self.sex), + "strain": self.strain, "sex": self.sex, "Genus_species": "{0} {1}".format(self.genus_uppercase, self.species_lowercase), "blast": self.blast, "go": self.go, "picture_path": self.picture_path} if (len(self.config.keys()) == 0): logging.error("Empty config dictionary") diff --git a/speciesData.py b/speciesData.py index b0d6190faeead7917f8efbb9a4a1341e198d5dc3..4826663d01374a1bac8c8801f7eb0f5030ac87a8 100755 --- a/speciesData.py +++ b/speciesData.py @@ -94,9 +94,9 @@ class SpeciesData: self.go = self.set_service_attribute(constants.ORG_PARAM_SERVICES_GO, parameters_dictionary) self.genus_lowercase = self.genus.lower() - self.species_lower = self.species.lower() + self.species_lowercase = self.species.lower() self.genus_uppercase = self.genus[0].upper() + self.genus_lowercase[1:] - self.genus_species = "{0}_{1}".format(self.genus_lowercase, self.species_lower) + self.genus_species = "{0}_{1}".format(self.genus_lowercase, self.species_lowercase) self.chado_species_name = "{0} {1}".format(self.species, self.sex) self.full_name = ' '.join(utilities.filter_empty_not_empty_items([self.genus_uppercase, self.species, self.strain, self.sex])["not_empty"]) @@ -104,14 +104,14 @@ class SpeciesData: self.abbreviation = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase[0], self.species, self.strain, self.sex])["not_empty"]) self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items( - [self.genus_lowercase, self.species_lower, self.strain.lower(), + [self.genus_lowercase, self.species_lowercase, self.strain.lower(), self.sex.lower()])["not_empty"]) self.dataset_prefix = None if self.sex is not None or self.sex != "": - self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lower + "_" + self.sex[0].lower() + self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lowercase + "_" + self.sex[0].lower() else: - self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lower + self.dataset_prefix = self.genus[0].lower() + "_" + self.species_lowercase # Bioblend/Chado IDs for an organism analyses/organisms/datasets/history/library self.org_id = None diff --git a/utilities.py b/utilities.py index 18d262335efab45efafb6c996eaabde8481e88e9..68a451374cbada2b0df616675d46b73727eee4c8 100755 --- a/utilities.py +++ b/utilities.py @@ -183,7 +183,7 @@ def get_sp_picture(sp_dict_list): if constants.ORG_PARAM_DESC_PICTURE_PATH in sp[constants.ORG_PARAM_DESC].keys() and \ sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_PICTURE_PATH] != "": sp_picture_dict[gspecies] = sp[constants.ORG_PARAM_DESC][constants.ORG_PARAM_DESC_PICTURE_PATH] - + print(sp_picture_dict) return sp_picture_dict def run_tool(instance, tool_id, history_id, tool_inputs):