From a12fe94f174da766be612fbb2712b4db2ba98296 Mon Sep 17 00:00:00 2001 From: lltommy Date: Wed, 22 Apr 2020 19:41:27 +0200 Subject: Small changes all around, trying to make the importer/metadata better --- scripts/from_genbank_to_fasta_and_yaml.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) (limited to 'scripts/from_genbank_to_fasta_and_yaml.py') diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index 00c0012..096a6af 100755 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -8,10 +8,11 @@ import json import os from datetime import date -today = date.today().strftime("%Y%m%d") +#today = date.today().strftime("%Y%m%d") -dir_metadata_today = 'metadata_from_nuccore_{}'.format(today) -dir_fasta_and_yaml_today = 'fasta_and_yaml_{}'.format(today) + +dir_metadata_today = 'metadata_from_nuccore' #_{}'.format(today) +dir_fasta_and_yaml_today = 'fasta_and_yaml' #'.format(today) dir_dict_ontology_standardization = 'dict_ontology_standardization/' @@ -177,7 +178,10 @@ if not os.path.exists(dir_fasta_and_yaml_today): if len(GBQualifier_value_text_list) > 1: if GBQualifier_value_text_list[1] in ['male', 'female']: - info_for_yaml_dict['host']['host_sex'] = GBQualifier_value_text_list[1] + if GBQualifier_value_text_list[1]=='male': + info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" + elif GBQualifier_value_text_list[1]=='female': + info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000383" else: info_for_yaml_dict['host']['host_health_status'] = GBQualifier_value_text_list[1] -- cgit v1.2.3