diff options
Diffstat (limited to 'scripts/download_genbank_data')
| -rwxr-xr-x | scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 12 |
1 files changed, 11 insertions, 1 deletions
diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py index 5a8a336..8fbacd1 100755 --- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py +++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py @@ -18,7 +18,7 @@ import json import os import requests -from datetime import date +from datetime import date, datetime from dateutil.parser import parse import sys @@ -27,6 +27,7 @@ from utils import is_integer, chunks, check_and_get_ontology_dictionaries num_ids_for_request = 100 +min_acceptable_collection_date = datetime(2019, 12, 1) dir_metadata = 'metadata_from_nuccore' dir_fasta_and_yaml = 'fasta_and_yaml' @@ -404,6 +405,15 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if accession_version not in not_created_accession_dict: not_created_accession_dict[accession_version] = [] not_created_accession_dict[accession_version].append('collection_date not found') + else: + year, month, day = [int(x) for x in info_for_yaml_dict['sample']['collection_date'].split('-')] + + collection_date_in_yaml = datetime(year, month, day) + + if collection_date_in_yaml < min_acceptable_collection_date: + if accession_version not in not_created_accession_dict: + not_created_accession_dict[accession_version] = [] + not_created_accession_dict[accession_version].append('collection_date too early') if 'authors' not in info_for_yaml_dict['submitter']: if accession_version not in not_created_accession_dict: |