diff options
Diffstat (limited to 'scripts/download_genbank_data')
| -rwxr-xr-x | scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py | 82 |
1 files changed, 30 insertions, 52 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 52aee4e..9b8fedc 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 @@ -16,11 +16,15 @@ import xml.etree.ElementTree as ET import json import os import requests -import sys from datetime import date from dateutil.parser import parse +import sys +sys.path.append('../') +from utils import is_integer, chunks, check_and_get_ontology_dictionaries + + num_ids_for_request = 100 dir_metadata = 'metadata_from_nuccore' @@ -30,16 +34,9 @@ dir_dict_ontology_standardization = args.dict_ontology today_date = date.today().strftime("%Y.%m.%d") path_ncbi_virus_accession = 'sequences.{}.acc'.format(today_date) -def is_integer(string_to_check): - try: - int(string_to_check) - return True - except ValueError: - return False -def chunks(lst, n): - for i in range(0, len(lst), n): - yield lst[i:i + n] +field_to_term_to_uri_dict = check_and_get_ontology_dictionaries(dir_dict_ontology_standardization) + if os.path.exists(dir_metadata): print("The directory '{}' already exists.".format(dir_metadata)) @@ -123,29 +120,10 @@ if not os.path.exists(dir_metadata): ) -term_to_uri_dict = {} - -for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_xxx_csv) for name_xxx_csv in os.listdir(dir_dict_ontology_standardization) if name_xxx_csv.endswith('.csv')]: - print('Read {}'.format(path_dict_xxx_csv)) - - with open(path_dict_xxx_csv) as f: - for line in f: - if len(line.split(',')) > 2: - term, uri = line.strip('\n').split('",') - else: - term, uri = line.strip('\n').split(',') - - term = term.strip('"') - - if term in term_to_uri_dict: - print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term)) - continue - - term_to_uri_dict[term] = uri - if not os.path.exists(dir_fasta_and_yaml): os.makedirs(dir_fasta_and_yaml) + min_len_to_count = 15000 num_seq_with_len_ge_X_bp = 0 @@ -166,7 +144,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) continue try: - #print(path_metadata_xxx_xml, accession_version) + # print(path_metadata_xxx_xml, accession_version) # A general default-empty yaml could be read from the definitive one info_for_yaml_dict = { @@ -230,8 +208,8 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) new_seq_tec_list = [] for seq_tec in tech_info_to_parse.split(';'): seq_tec = seq_tec.strip() - if seq_tec in term_to_uri_dict: - seq_tec = term_to_uri_dict[seq_tec] + if seq_tec in field_to_term_to_uri_dict['ncbi_sequencing_technology']: + seq_tec = field_to_term_to_uri_dict['ncbi_sequencing_technology'][seq_tec] new_seq_tec_list.append(seq_tec) else: missing_value_list.append('\t'.join([accession_version, 'sample_sequencing_technology', seq_tec])) @@ -256,17 +234,17 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if GBQualifier_name_text == 'host': GBQualifier_value_text = GBQualifier_value_text.split(';')[0] # For case like Homo sapiens;sex:female - if GBQualifier_value_text in term_to_uri_dict: + if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_host_species']: # Cases like 'Felis catus; Domestic Shorthair' - info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[GBQualifier_value_text] + info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][GBQualifier_value_text] else: GBQualifier_value_text_list = GBQualifier_value_text.split('; ') - if GBQualifier_value_text_list[0] in term_to_uri_dict: - info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[GBQualifier_value_text_list[0]] + if GBQualifier_value_text_list[0] in field_to_term_to_uri_dict['ncbi_host_species']: + info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][GBQualifier_value_text_list[0]] elif GBQualifier_value_text_list[0] and ('MT215193' in accession_version or 'MT270814' in accession_version): # Information checked manually from NCBI Virus - info_for_yaml_dict['host']['host_species'] = term_to_uri_dict['Canis lupus familiaris'] + info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species']['Canis lupus familiaris'] else: missing_value_list.append('\t'.join([accession_version, 'host_species', GBQualifier_value_text_list[0]])) @@ -295,8 +273,8 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if host_sex in ['male', 'female']: info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" if host_sex == 'male' else "http://purl.obolibrary.org/obo/PATO_0000383" - elif GBQualifier_value_text_list[1] in term_to_uri_dict: - info_for_yaml_dict['host']['host_health_status'] = term_to_uri_dict[GBQualifier_value_text_list[1]] + elif GBQualifier_value_text_list[1] in field_to_term_to_uri_dict['ncbi_host_health_status']: + info_for_yaml_dict['host']['host_health_status'] = field_to_term_to_uri_dict['ncbi_host_health_status'][GBQualifier_value_text_list[1]] else: missing_value_list.append('\t'.join([accession_version, 'host_sex or host_health_status', GBQualifier_value_text_list[1]])) @@ -318,25 +296,25 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) else: info_for_yaml_dict['sample']['collector_name'] = GBQualifier_value_text elif GBQualifier_name_text == 'isolation_source': - if GBQualifier_value_text.upper() in term_to_uri_dict: - GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa' + if GBQualifier_value_text.upper() in field_to_term_to_uri_dict['ncbi_speciesman_source']: + GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa' # Little cleaning GBQualifier_value_text = GBQualifier_value_text.strip("/'") - if GBQualifier_value_text in term_to_uri_dict: - info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[GBQualifier_value_text]] + if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_speciesman_source']: + info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source'][GBQualifier_value_text]] else: if GBQualifier_value_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'combined nasopharyngeal and oropharyngeal swab', 'naso and/or oropharyngeal swab']: - info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['oropharyngeal swab']] + info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal swab']] elif GBQualifier_value_text.lower() in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab', 'nasopharyngeal aspirate/throat swab', 'Nasopharyngeal/Throat']: - info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']] + info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']] elif GBQualifier_value_text.lower() in ['nasopharyngeal aspirate & throat swab', 'nasopharyngeal aspirate and throat swab']: - info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal aspirate'], term_to_uri_dict['throat swab']] + info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasopharyngeal aspirate'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']] elif GBQualifier_value_text.lower() in ['nasal swab and throat swab']: - info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['throat swab']] + info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['throat swab']] elif GBQualifier_value_text.lower() in ['nasal-swab and oro-pharyngeal swab']: - info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['oropharyngeal swab']] + info_for_yaml_dict['sample']['specimen_source'] = [field_to_term_to_uri_dict['ncbi_speciesman_source']['nasal swab'], field_to_term_to_uri_dict['ncbi_speciesman_source']['oropharyngeal swab']] else: missing_value_list.append('\t'.join([accession_version, 'specimen_source', GBQualifier_value_text])) elif GBQualifier_name_text == 'collection_date': @@ -371,8 +349,8 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) if GBQualifier_name_text == 'country' and ': ' in GBQualifier_value_text: GBQualifier_value_text = GBQualifier_value_text.replace(': ', ':') - if GBQualifier_value_text in term_to_uri_dict: - info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[GBQualifier_value_text] + if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_countries']: + info_for_yaml_dict['sample']['collection_location'] = field_to_term_to_uri_dict['ncbi_countries'][GBQualifier_value_text] else: missing_value_list.append('\t'.join([accession_version, GBQualifier_name_text, GBQualifier_value_text])) elif GBQualifier_name_text == 'note': @@ -387,7 +365,7 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) # Check if mandatory fields are missing if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']: - #print(accession_version, ' - technology not found') + # print(accession_version, ' - technology not found') if accession_version not in not_created_accession_dict: not_created_accession_dict[accession_version] = [] not_created_accession_dict[accession_version].append('sample_sequencing_technology not found') |