diff options
Diffstat (limited to 'scripts/create_sra_metadata/create_sra_metadata.py')
| -rw-r--r-- | scripts/create_sra_metadata/create_sra_metadata.py | 65 |
1 files changed, 21 insertions, 44 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index b872896..d94093e 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -14,7 +14,10 @@ from dateutil.parser import parse import xml.etree.ElementTree as ET import json import gzip + import sys +sys.path.append('../') +from utils import is_integer, check_and_get_ontology_dictionaries dir_yaml = 'yaml' @@ -29,14 +32,6 @@ dir_dict_ontology_standardization = args.dict_ontology path_sra_study_accessions_txt = 'SRAStudyAccessions.{}.txt'.format(date) -def is_integer(string_to_check): - try: - int(string_to_check) - return True - except ValueError: - return False - - accession_to_ignore_set = set() if args.ids_to_ignore: @@ -64,25 +59,7 @@ if args.ids_to_consider: print('There are {} accessions to consider.'.format(len(accession_to_consider_set))) -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 +field_to_term_to_uri_dict = check_and_get_ontology_dictionaries(dir_dict_ontology_standardization) if not os.path.exists(dir_yaml): @@ -151,13 +128,13 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): if VALUE_text.lower() in ['homo sapien', 'homosapiens']: VALUE_text = 'Homo sapiens' - if VALUE_text in term_to_uri_dict: - info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[VALUE_text] + if VALUE_text 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'][VALUE_text] else: missing_value_list.append('\t'.join([accession, 'host_species', VALUE_text])) elif TAG_text in ['host_health_status', 'host health state']: - if VALUE_text in term_to_uri_dict: - info_for_yaml_dict['host']['host_health_status'] = term_to_uri_dict[VALUE_text] + if VALUE_text 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'][VALUE_text] elif VALUE_text.strip("'") not in ['missing', 'not collected', 'not provided']: missing_value_list.append('\t'.join([accession, 'host_health_status', VALUE_text])) elif TAG_text in ['strain', 'isolate']: @@ -167,27 +144,27 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): if value_to_insert.lower() in ['homo sapien', 'homosapiens']: value_to_insert = 'Homo sapiens' - if value_to_insert in term_to_uri_dict: - value_to_insert = term_to_uri_dict[value_to_insert] + if value_to_insert in field_to_term_to_uri_dict['ncbi_host_species']: + value_to_insert = field_to_term_to_uri_dict['ncbi_host_species'][value_to_insert] if 'virus_strain' not in info_for_yaml_dict: info_for_yaml_dict['virus']['virus_strain'] = value_to_insert else: info_for_yaml_dict['virus']['virus_strain'] += '; ' + value_to_insert elif TAG_text in ['isolation_source', 'isolation source host-associated']: - if VALUE_text in term_to_uri_dict: - info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[VALUE_text]] + if 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'][VALUE_text]] else: if 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 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 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 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 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']] elif VALUE_text.strip("'") not in ['missing', 'not collected', 'unknown', 'not provided', 'not applicable', 'N/A']: missing_value_list.append('\t'.join([accession, 'specimen_source', VALUE_text])) elif TAG_text in ['host_sex', 'host sex']: @@ -238,8 +215,8 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): if ': ' in VALUE_text: VALUE_text = VALUE_text.replace(': ', ':') - if VALUE_text in term_to_uri_dict: - info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[VALUE_text] + if 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'][VALUE_text] elif VALUE_text.lower() not in ['na', 'not applicable']: missing_value_list.append('\t'.join([accession, 'geo_loc_name', VALUE_text])) #else: @@ -255,8 +232,8 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): INSTRUMENT_MODEL = [x.text for x in EXPERIMENT.find('PLATFORM').iter('INSTRUMENT_MODEL')][0] if INSTRUMENT_MODEL.lower() != 'unspecified': - if INSTRUMENT_MODEL in term_to_uri_dict: - info_for_yaml_dict['technology']['sample_sequencing_technology'] = [term_to_uri_dict[INSTRUMENT_MODEL]] + if INSTRUMENT_MODEL in field_to_term_to_uri_dict['ncbi_sequencing_technology']: + info_for_yaml_dict['technology']['sample_sequencing_technology'] = [field_to_term_to_uri_dict['ncbi_sequencing_technology'][INSTRUMENT_MODEL]] else: missing_value_list.append('\t'.join([accession, 'sample_sequencing_technology', INSTRUMENT_MODEL])) #else: |