#!/usr/bin/env python3
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--ids-to-ignore', type=str, help='file with ids to ignore in all steps, 1 id per line', required=False)
parser.add_argument('--ids-to-consider', type=str, help='file with ids to consider in all steps, 1 id per line', required=False)
parser.add_argument('--dict-ontology', type=str, help='where is the ontology',
default='../dict_ontology_standardization/', required=False)
args = parser.parse_args()
import os
from dateutil.parser import parse
import xml.etree.ElementTree as ET
import json
import gzip
from datetime import datetime
import sys
sys.path.append('../')
from utils import is_integer, check_and_get_ontology_dictionaries
dir_yaml = 'yaml'
date = '2020.07.09'
min_acceptable_collection_date = datetime(2019, 12, 1)
# Query on SRA: 'txid2697049[Organism]' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism%5D)
# Query on SRA: 'txid2697049[Organism:noexp] NOT 0[Mbases ' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism:noexp%5D%20NOT%200[Mbases)
# -> Send to -> File -> Full XML -> Create File
path_sra_metadata_xml = 'SraExperimentPackage.{}.xml.gz'.format(date)
dir_dict_ontology_standardization = args.dict_ontology
path_sra_study_accessions_txt = 'SRAStudyAccessions.{}.txt'.format(date)
accession_to_ignore_set = set()
if args.ids_to_ignore:
if not os.path.exists(args.ids_to_ignore):
print("\tThe '{}' file doesn't exist.".format(args.ids_to_ignore))
sys.exit(-1)
with open(args.ids_to_ignore) as f:
accession_to_ignore_set.update(set([x.split('.')[0] for x in f.read().strip('\n').split('\n')]))
print('There are {} accessions to ignore.'.format(len(accession_to_ignore_set)))
accession_to_consider_set = set()
if args.ids_to_consider:
if not os.path.exists(args.ids_to_consider):
print("\tThe '{}' file doesn't exist.".format(args.ids_to_consider))
sys.exit(-1)
with open(args.ids_to_consider) as f:
accession_to_consider_set.update(set([x.split('.')[0] for x in f.read().strip('\n').split('\n')]))
if len(accession_to_consider_set) > 0:
print('There are {} accessions to consider.'.format(len(accession_to_consider_set)))
field_to_term_to_uri_dict = check_and_get_ontology_dictionaries(dir_dict_ontology_standardization)
if not os.path.exists(dir_yaml):
os.makedirs(dir_yaml)
sra_metadata_xml_file = gzip.open(path_sra_metadata_xml, 'r')
tree = ET.parse(sra_metadata_xml_file)
sra_metadata_xml_file.close()
EXPERIMENT_PACKAGE_SET = tree.getroot()
missing_value_list = []
not_created_accession_dict = {}
run_accession_set = set()
run_accession_to_downloadble_file_url_dict = {}
num_yaml_created = 0
for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
#print(i, EXPERIMENT_PACKAGE)
# A general default-empty yaml could be read from the definitive one
info_for_yaml_dict = {
'id': 'placeholder',
'host': {},
'sample': {},
'virus': {},
'technology': {},
'submitter': {}
}
RUN_SET = EXPERIMENT_PACKAGE.find('RUN_SET')
RUN = RUN_SET.find('RUN')
accession = RUN.attrib['accession']
run_accession_set.add(accession)
#print(accession)
if accession in accession_to_ignore_set:
continue
if len(accession_to_consider_set) > 0 and accession not in accession_to_consider_set:
continue
info_for_yaml_dict['sample']['sample_id'] = accession
#SRAFiles = RUN.find('SRAFiles')
#if SRAFiles is not None:
# url = SRAFiles.find('SRAFile').attrib['url']
# if 'sra-download.ncbi.nlm.nih.gov' in url:
# run_accession_to_downloadble_file_url_dict[accession] = url
SAMPLE = EXPERIMENT_PACKAGE.find('SAMPLE')
SAMPLE_ATTRIBUTE_list = SAMPLE.iter('SAMPLE_ATTRIBUTE')
for SAMPLE_ATTRIBUTE in SAMPLE_ATTRIBUTE_list:
VALUE = SAMPLE_ATTRIBUTE.find('VALUE')
if VALUE is not None:
TAG_text = SAMPLE_ATTRIBUTE.find('TAG').text
VALUE_text = VALUE.text
if TAG_text in ['host', 'host scientific name']:
if VALUE_text.lower() in ['homo sapien', 'homosapiens']:
VALUE_text = 'Homo sapiens'
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 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']:
if VALUE_text.lower() not in ['not applicable', 'missing', 'na', 'unknown', 'not provided']:
value_to_insert = VALUE_text
if value_to_insert.lower() in ['homo sapien', 'homosapiens']:
value_to_insert = 'Homo sapiens'
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 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', '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'] = [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'] = [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'] = [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'] = [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'] = [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']:
if VALUE_text.lower() not in ['missing', 'not provided']:
if VALUE_text in ['male', 'female']:
info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" if VALUE_text == 'male' else "http://purl.obolibrary.org/obo/PATO_0000383"
else:
missing_value_list.append('\t'.join([accession, 'host_sex', VALUE_text]))
elif TAG_text in ['host_age', 'host age']:
if is_integer(VALUE_text):
host_age = int(VALUE_text)
if host_age >= 0 and host_age < 110:
info_for_yaml_dict['host']['host_age'] = host_age
info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036'
elif TAG_text == 'collected_by':
if VALUE_text.lower() not in ['not available', 'missing']:
name = VALUE_text in ['Dr. Susie Bartlett', 'Ahmed Babiker', 'Aisi Fu', 'Brandi Williamson', 'George Taiaroa', 'Natacha Ogando', 'Tim Dalebout', 'ykut Ozdarendeli']
info_for_yaml_dict['sample']['collector_name' if name else 'collecting_institution'] = VALUE_text
elif TAG_text == 'collecting institution':
if VALUE_text.lower() not in ['not provided', 'na']:
info_for_yaml_dict['sample']['collecting_institution'] = VALUE_text
elif TAG_text in ['collection_date', 'collection date']:
if VALUE_text.lower() not in ['not applicable', 'missing', 'na']:
date_to_write = VALUE_text
date_is_estimated = True
VALUE_text_list = VALUE_text.split('-')
if len(VALUE_text_list) == 3:
date_is_estimated = False
if VALUE_text_list[1].isalpha():
date_to_write = parse(VALUE_text).strftime('%Y-%m-%d')
elif len(VALUE_text_list) == 2:
date_to_write = parse(VALUE_text).strftime('%Y-%m') + '-15'
else:
if int(VALUE_text) < 2020:
date_to_write = "{}-12-15".format(VALUE_text)
else:
date_to_write = "{}-01-15".format(VALUE_text)
info_for_yaml_dict['sample']['collection_date'] = date_to_write
if date_is_estimated:
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(VALUE_text)
else:
info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(VALUE_text)
elif TAG_text in ['geo_loc_name', 'geographic location (country and/or sea)', 'geographic location (region and locality)']:
if ': ' in VALUE_text:
VALUE_text = VALUE_text.replace(': ', ':')
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:
# if TAG_text not in ['lat_lon', 'host_disease', 'BioSampleModel', 'passage_history']:
# print(accession, TAG_text, VALUE_text)
taxon_id = SAMPLE.find('SAMPLE_NAME').find('TAXON_ID').text
info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_" + taxon_id
# This script download and prepare data and metadata for samples that will be mapped against a referenceT
info_for_yaml_dict['technology']['assembly_method'] = 'http://purl.obolibrary.org/obo/GENEPIO_0002028'
EXPERIMENT = EXPERIMENT_PACKAGE.find('EXPERIMENT')
INSTRUMENT_MODEL = [x.text for x in EXPERIMENT.find('PLATFORM').iter('INSTRUMENT_MODEL')][0]
if INSTRUMENT_MODEL.lower() != 'unspecified':
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:
# print(accession, 'Missing INSTRUMENT_MODEL', info_for_yaml_dict)
LIBRARY_DESCRIPTOR = EXPERIMENT.find('DESIGN').find('LIBRARY_DESCRIPTOR')
if LIBRARY_DESCRIPTOR.text not in ['', 'OTHER']:
info_for_yaml_dict['technology']['additional_technology_information'] = 'LIBRARY_STRATEGY: {};'.format(LIBRARY_DESCRIPTOR.find('LIBRARY_STRATEGY').text)
SUBMISSION = EXPERIMENT_PACKAGE.find('SUBMISSION')
if SUBMISSION.attrib['accession']:
info_for_yaml_dict['submitter']['submitter_sample_id'] = SUBMISSION.attrib['accession']
if SUBMISSION.attrib['lab_name'].lower() not in ['', 'na']:
info_for_yaml_dict['submitter']['originating_lab'] = SUBMISSION.attrib['lab_name']
STUDY = EXPERIMENT_PACKAGE.find('STUDY')
if STUDY.attrib['alias']:
info_for_yaml_dict['submitter']['publication'] = STUDY.attrib['alias']
Organization = EXPERIMENT_PACKAGE.find('Organization')
Organization_Name = Organization.find('Name')
if Organization_Name.text:
info_for_yaml_dict['submitter']['authors'] = [Organization_Name.text]
Organization_Contact = Organization.find('Contact')
if Organization_Contact is not None:
Organization_Contact_Name = Organization_Contact.find('Name')
info_for_yaml_dict['submitter']['submitter_name'] = [Organization_Contact_Name.find('First').text + ' ' + Organization_Contact_Name.find('Last').text]
info_for_yaml_dict['submitter']['additional_submitter_information'] = Organization_Contact.attrib['email']
Organization_Concact_Address = Organization_Contact.find('Address')
if Organization_Concact_Address is not None:
info_for_yaml_dict['submitter']['submitter_address'] = '; '.join([x.text for x in Organization_Concact_Address] + ['Postal code ' + Organization_Concact_Address.attrib['postal_code']])
Organization_Address = Organization.find('Address')
if Organization_Address is not None:
info_for_yaml_dict['submitter']['lab_address'] = '; '.join([x.text for x in Organization_Address] + ['Postal code ' + Organization_Address.attrib['postal_code']])
# Do not trick the quality control!
#if 'collection_date' not in info_for_yaml_dict['sample']:
# info_for_yaml_dict['sample']['collection_date'] = '1970-01-01'
# info_for_yaml_dict['sample']['additional_collection_information'] = "The real 'collection_date' is missing"
# Check if mandatory fields are missing
if 'collection_date' not in info_for_yaml_dict['sample']:
# print(accession_version, ' - collection_date not found')
if accession not in not_created_accession_dict:
not_created_accession_dict[accession] = []
not_created_accession_dict[accession].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 not in not_created_accession_dict:
not_created_accession_dict[accession] = []
not_created_accession_dict[accession].append('collection_date too early')
if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']:
# print(accession_version, ' - technology not found')
if accession not in not_created_accession_dict:
not_created_accession_dict[accession] = []
not_created_accession_dict[accession].append('sample_sequencing_technology not found')
if 'collection_location' not in info_for_yaml_dict['sample']:
if accession not in not_created_accession_dict:
not_created_accession_dict[accession] = []
not_created_accession_dict[accession].append('collection_location not found')
if 'collection_date' not in info_for_yaml_dict['sample']:
if accession not in not_created_accession_dict:
not_created_accession_dict[accession] = []
not_created_accession_dict[accession].append('collection_date not found')
if 'authors' not in info_for_yaml_dict['submitter']:
if accession not in not_created_accession_dict:
not_created_accession_dict[accession] = []
not_created_accession_dict[accession].append('authors not found')
if 'host_species' not in info_for_yaml_dict['host']:
if accession not in not_created_accession_dict:
not_created_accession_dict[accession] = []
not_created_accession_dict[accession].append('host_species not found')
if accession not in not_created_accession_dict:
num_yaml_created += 1
with open(os.path.join(dir_yaml, '{}.yaml'.format(accession)), 'w') as fw:
json.dump(info_for_yaml_dict, fw, indent=2)
if len(missing_value_list) > 0:
path_missing_terms_tsv = 'missing_terms.sra.tsv'
print('Written missing terms in {}'.format(path_missing_terms_tsv))
with open(path_missing_terms_tsv, 'w') as fw:
fw.write('\n'.join(missing_value_list))
if len(not_created_accession_dict) > 0:
path_not_created_accession_tsv = 'not_created_accession.sra.tsv'
print('Written not created accession in {}'.format(path_not_created_accession_tsv))
with open(path_not_created_accession_tsv, 'w') as fw:
fw.write('\n'.join(['\t'.join([accession_version, ','.join(missing_info_list)]) for accession_version, missing_info_list in not_created_accession_dict.items()]))
print('Num. YAML files created: {}'.format(num_yaml_created))
