diff options
| -rwxr-xr-x | scripts/from_genbank_to_fasta_and_yaml.py | 34 |
1 files changed, 32 insertions, 2 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py index 21ed3b2..0175d3c 100755 --- a/scripts/from_genbank_to_fasta_and_yaml.py +++ b/scripts/from_genbank_to_fasta_and_yaml.py @@ -7,6 +7,8 @@ import xml.etree.ElementTree as ET import json import os +from dateutil import parser + num_ids_for_request = 100 dir_metadata = 'metadata_from_nuccore' @@ -221,7 +223,32 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) missing_value_list.append('\t'.join([accession_version, 'specimen_source', GBQualifier_value_text])) elif GBQualifier_name_text == 'collection_date': # TO_DO: which format we will use? - info_for_yaml_dict['sample']['collection_date'] = GBQualifier_value_text + date_to_write = GBQualifier_value_text + + if len(GBQualifier_value_text.split('-')) == 1: + if int(GBQualifier_value_text) < 2020: + date_to_write = "15 12 {}".format(GBQualifier_value_text) + else: + date_to_write = "15 01 {}".format(GBQualifier_value_text) + + if 'additional_collection_information' in info_for_yaml_dict['sample']: + info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text) + else: + info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text) + elif len(GBQualifier_value_text.split('-')) == 2: + date_to_write += '-15' + + if 'additional_collection_information' in info_for_yaml_dict['sample']: + info_for_yaml_dict['sample']['additional_collection_information'] += "; The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text) + else: + info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(GBQualifier_value_text) + elif len(GBQualifier_value_text.split('-')) == 3: + GBQualifier_value_text_list = GBQualifier_value_text.split('-') + + if GBQualifier_value_text_list[1].isalpha(): + date_to_write = GBQualifier_value_text_list[1] + ' ' + GBQualifier_value_text_list[0] + ' ' + GBQualifier_value_text_list[2] + + info_for_yaml_dict['sample']['collection_date'] = date_to_write elif GBQualifier_name_text in ['lat_lon', 'country']: if GBQualifier_value_text == 'Hong Kong': GBQualifier_value_text = 'China: Hong Kong' @@ -233,7 +260,10 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) info_for_yaml_dict['sample']['collection_location'] = GBQualifier_value_text elif GBQualifier_name_text == 'note': - info_for_yaml_dict['sample']['additional_collection_information'] = GBQualifier_value_text + if 'additional_collection_information' in info_for_yaml_dict['sample']: + info_for_yaml_dict['sample']['additional_collection_information'] += '; ' + GBQualifier_value_text + else: + info_for_yaml_dict['sample']['additional_collection_information'] = GBQualifier_value_text elif GBQualifier_name_text == 'isolate': info_for_yaml_dict['virus']['virus_strain'] = GBQualifier_value_text elif GBQualifier_name_text == 'db_xref': |