diff --git a/gga_get_data.py b/gga_get_data.py index 9950a86b35a4728b57484859d3964bc2d49c34a7..992e5c6c46f59d0bfdd2cecf14f99d3be21f0a95 100755 --- a/gga_get_data.py +++ b/gga_get_data.py @@ -88,18 +88,14 @@ class GetData(speciesData.SpeciesData): organism_annotation_dir = os.path.abspath("./src_data/annotation/{0}/OGS{1}".format(self.species_folder_name, self.ogs_version)) organism_genome_dir = os.path.abspath("./src_data/genome/{0}/v{1}".format(self.species_folder_name, self.genome_version)) - genome_datasets = [constants.ORG_PARAM_DATA_GENOME_PATH] - annotation_datasets = [constants.ORG_PARAM_DATA_GFF_PATH, - constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH, - constants.ORG_PARAM_DATA_PROTEINS_PATH, - constants.ORG_PARAM_DATA_INTERPRO_PATH, - constants.ORG_PARAM_DATA_ORTHOFINDER_PATH, - constants.ORG_PARAM_DATA_BLASTP_PATH, - constants.ORG_PARAM_DATA_BLASTX_PATH] - # Where to store blast results? - - # search_excluded_datasets = ["interpro_path", "orthofinder_path", "blastp_path", "blastx_path"] - # These datasets will not be searched if missing in the input file + genome_datasets = {constants.ORG_PARAM_DATA_GENOME_PATH: self.genome_path} + annotation_datasets = {constants.ORG_PARAM_DATA_GFF_PATH: self.gff_path, + constants.ORG_PARAM_DATA_TRANSCRIPTS_PATH: self.transcripts_path, + constants.ORG_PARAM_DATA_PROTEINS_PATH: self.proteins_path, + constants.ORG_PARAM_DATA_INTERPRO_PATH: self.interpro_path, + constants.ORG_PARAM_DATA_ORTHOFINDER_PATH: self.orthofinder_path, + constants.ORG_PARAM_DATA_BLASTP_PATH: self.blastp_path, + constants.ORG_PARAM_DATA_BLASTX_PATH: self.blastx_path} # Copy datasets in the organism src_data dir tree correct folder for k, v in genome_datasets.items(): diff --git a/utilities.py b/utilities.py index 3e23ef4deb8a62fe56431015c68a3b0d00e88395..3d734f24a9c9bdd82f60f6127a051602493b861b 100755 --- a/utilities.py +++ b/utilities.py @@ -37,7 +37,7 @@ def parse_config(config_file): config_dict = load_yaml(config_file) if isinstance(config_dict, dict): - logging.debug("Config dictionary: {0}".format(config_dict)) + #logging.debug("Config dictionary: {0}".format(config_dict)) return config_dict else: logging.critical("Config yaml file is not a dictionary" % config_file)