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#!/usr/bin/env python3
from Bio import Entrez
Entrez.email = 'another_email@gmail.com'
import xml.etree.ElementTree as ET
import json
import os
import requests
from datetime import date
from dateutil.parser import parse
num_ids_for_request = 100
dir_metadata = 'metadata_from_nuccore'
dir_fasta_and_yaml = 'fasta_and_yaml'
dir_dict_ontology_standardization = 'dict_ontology_standardization/'
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]
if not os.path.exists(dir_metadata):
os.makedirs(dir_metadata)
# Take all the ids
id_set = set()
# Try to search several strings
term_list = ['SARS-CoV-2', 'SARS-CoV2', 'SARS CoV2', 'SARSCoV2', 'txid2697049[Organism]']
for term in term_list:
tmp_list = Entrez.read(
Entrez.esearch(db='nuccore', term=term, idtype='acc', retmax='10000')
)['IdList']
# Remove mRNAs, ncRNAs, Proteins, and predicted models (more information here: https://en.wikipedia.org/wiki/RefSeq)
tmp_list = [x for x in tmp_list if x[:2] not in ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP']]
# Remove the version in the id
tmp_list = [x.split('.')[0] for x in tmp_list]
#tmp_list = tmp_list[0:2] # restricting to small run
new_ids_set = set([x.split('.')[0] for x in tmp_list])
new_ids = len(new_ids_set.difference(id_set))
id_set.update(new_ids_set)
print('Term:', term, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set))
if not os.path.exists(path_ncbi_virus_accession):
r = requests.get('https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/?q=*:*&fq=%7B!tag=SeqType_s%7DSeqType_s:(%22Nucleotide%22)&fq=VirusLineageId_ss:(2697049)&cmd=download&sort=SourceDB_s%20desc,CreateDate_dt%20desc,id%20asc&dlfmt=acc&fl=id')
with open(path_ncbi_virus_accession, 'w') as fw:
fw.write(r.text)
with open(path_ncbi_virus_accession) as f:
tmp_list = [line.strip('\n') for line in f]
new_ids = len(set(tmp_list).difference(id_set))
id_set.update(tmp_list)
print('DB: NCBI Virus', today_date, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set))
for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)):
path_metadata_xxx_xml = os.path.join(dir_metadata, 'metadata_{}.xml'.format(i))
print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xxx_xml))
with open(path_metadata_xxx_xml, 'w') as fw:
fw.write(
Entrez.efetch(db='nuccore', id=id_x_list, retmode='xml').read()
)
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('",')
term = term.strip('"')
else:
term, uri = line.strip('\n').split(',')
term_to_uri_dict[term] = uri
species_to_taxid_dict = {
'Homo sapiens': 'http://purl.obolibrary.org/obo/NCBITaxon_9606',
'Mustela lutreola': 'http://purl.obolibrary.org/obo/NCBITaxon_9666',
'Manis javanica': 'http://purl.obolibrary.org/obo/NCBITaxon_9974',
'Felis catus': 'http://purl.obolibrary.org/obo/NCBITaxon_9685',
'Panthera tigris jacksoni': 'http://purl.obolibrary.org/obo/NCBITaxon_419130',
'Canis lupus familiaris': 'http://purl.obolibrary.org/obo/NCBITaxon_9615'
}
if not os.path.exists(dir_fasta_and_yaml):
os.makedirs(dir_fasta_and_yaml)
min_len_to_count = 27500
num_seq_with_len_ge_X_bp = 0
missing_value_list = []
for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata) if name_metadata_xxx_xml.endswith('.xml')]:
tree = ET.parse(path_metadata_xxx_xml)
GBSet = tree.getroot()
for GBSeq in GBSet:
accession_version = GBSeq.find('GBSeq_accession-version').text
GBSeq_sequence = GBSeq.find('GBSeq_sequence')
if GBSeq_sequence is None:
print(accession_version, ' - sequence not found')
continue
#print(path_metadata_xxx_xml, accession_version)
# A general default-empty yaml could be read from the definitive one
info_for_yaml_dict = {
'id': 'placeholder',
'host': {},
'sample': {},
'virus': {},
'technology': {},
'submitter': {}
}
info_for_yaml_dict['sample']['sample_id'] = accession_version
info_for_yaml_dict['sample']['source_database_accession'] = ["http://identifiers.org/insdc/"+accession_version+"#sequence"] #accession is turned into resolvable URL/URI now
# submitter info
GBSeq_references = GBSeq.find('GBSeq_references')
if GBSeq_references is not None:
info_for_yaml_dict['submitter']['authors'] = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')]
GBReference = GBSeq_references.find('GBReference')
if GBReference is not None:
GBReference_journal = GBReference.find('GBReference_journal')
if GBReference_journal is not None and GBReference_journal.text != 'Unpublished':
if 'Submitted' in GBReference_journal.text:
info_for_yaml_dict['submitter']['submitter_name'] = ["{}".format(GBReference_journal.text.split(') ')[1].split(',')[0].strip())]
info_for_yaml_dict['submitter']['submitter_address'] = ','.join(GBReference_journal.text.split(') ')[1].split(',')[1:]).strip()
else:
info_for_yaml_dict['submitter']['additional_submitter_information'] = GBReference_journal.text
GBSeq_comment = GBSeq.find('GBSeq_comment')
if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text:
prefix_split_string = '##Genome-Assembly' if GBSeq_comment.text.startswith('##Genome-') else '##Assembly'
GBSeq_comment_text = GBSeq_comment.text.split(
'{}-Data-START## ; '.format(prefix_split_string)
)[1].split(' ; {}-Data-END##'.format(prefix_split_string))[0]
for info_to_check, field_in_yaml in zip(
['Assembly Method', 'Coverage', 'Sequencing Technology'],
['sequence_assembly_method', 'sequencing_coverage', 'sample_sequencing_technology']
):
if info_to_check in GBSeq_comment_text:
tech_info_to_parse = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0]
if field_in_yaml == 'sequencing_coverage':
# A regular expression would be better!
try:
info_for_yaml_dict['technology'][field_in_yaml] = [
float(tech_info_to_parse.strip('(average)').strip("reads/nt").strip('(average for 6 sequences)').replace(',', '.').strip(' xX>'))
]
except ValueError:
print(accession_version, "Couldn't make sense of Coverage '%s'" % tech_info_to_parse)
pass
elif field_in_yaml == 'sample_sequencing_technology':
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]
else:
missing_value_list.append('\t'.join([accession_version, 'sample_sequencing_technology', seq_tec]))
new_seq_tec_list.append(seq_tec)
info_for_yaml_dict['technology']['sample_sequencing_technology'] = [x for x in new_seq_tec_list]
else:
info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse
for GBFeature in GBSeq.iter('GBFeature'):
if GBFeature.find('GBFeature_key').text != 'source':
continue
for GBQualifier in GBFeature.iter('GBQualifier'):
GBQualifier_value = GBQualifier.find('GBQualifier_value')
if GBQualifier_value is None:
continue
GBQualifier_value_text = GBQualifier_value.text
GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text
if GBQualifier_name_text == 'host':
GBQualifier_value_text_list = GBQualifier_value_text.split('; ')
if GBQualifier_value_text_list[0] in species_to_taxid_dict:
info_for_yaml_dict['host']['host_species'] = species_to_taxid_dict[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'] = species_to_taxid_dict['Canis lupus familiaris']
else:
missing_value_list.append('\t'.join([accession_version, 'host_species', GBQualifier_value_text_list[0]]))
# Possible cases:
# - Homo sapiens --> ['Homo sapiens']
# - Homo sapiens; female --> ['Homo sapiens', 'female']
# - Homo sapiens; female 63 --> ['Homo sapiens', 'female 63']
# - Homo sapiens; female; age 40 --> ['Homo sapiens', 'female', 'age 40']
# - Homo sapiens; gender: F; age: 61 --> ['Homo sapiens', 'gender: F', 'age: 61']
# - Homo sapiens; gender: M; age: 68 --> ['Homo sapiens', 'gender: M', 'age: 68']
# - Homo sapiens; hospitalized patient --> ['Homo sapiens', 'hospitalized patient']
# - Homo sapiens; male --> ['Homo sapiens', 'male']
# - Homo sapiens; male; 63 --> ['Homo sapiens', 'male', '63']
# - Homo sapiens; male; age 29 --> ['Homo sapiens', 'male', 'age 29']
# - Homo sapiens; symptomatic --> ['Homo sapiens', 'symptomatic']
if len(GBQualifier_value_text_list) > 1:
host_sex = ''
if 'female' in GBQualifier_value_text_list[1]:
host_sex = 'female'
elif 'male' in GBQualifier_value_text_list[1]:
host_sex = 'male'
elif 'gender' in GBQualifier_value_text_list[1]:
host_sex_one_lecter = GBQualifier_value_text_list[1].split(':')[-1].strip()
if host_sex_one_lecter in ['F', 'M']:
host_sex = 'female' if host_sex_one_lecter == 'F' else 'male'
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]]
else:
missing_value_list.append('\t'.join([accession_version, 'host_sex or host_health_status', GBQualifier_value_text_list[1]]))
# Host age
host_age = -1
if len(GBQualifier_value_text_list[1].split(' ')) > 1 and is_integer(GBQualifier_value_text_list[1].split(' ')[-1]):
host_age = int(GBQualifier_value_text_list[1].split(' ')[-1])
elif len(GBQualifier_value_text_list) > 2 and is_integer(GBQualifier_value_text_list[2].split(' ')[-1]):
host_age = int(GBQualifier_value_text_list[2].split(' ')[-1])
if host_age > -1:
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 len(GBQualifier_value_text_list) > 2:
missing_value_list.append('\t'.join([accession_version, 'host_age', GBQualifier_value_text_list[2]]))
elif GBQualifier_name_text == 'collected_by':
if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]):
info_for_yaml_dict['sample']['collecting_institution'] = GBQualifier_value_text
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'
# 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]]
else:
if GBQualifier_value_text.lower() in ['np/op', 'np/op swab', 'np/np swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab']:
info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['oropharyngeal swab']]
elif GBQualifier_value_text in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab']:
info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal swab'], term_to_uri_dict['throat swab']]
elif GBQualifier_value_text in ['nasopharyngeal aspirate/throat swab']:
info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasopharyngeal aspirate'], term_to_uri_dict['throat swab']]
else:
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?
date_to_write = GBQualifier_value_text
if len(GBQualifier_value_text.split('-')) == 1:
if int(GBQualifier_value_text) < 2020:
date_to_write = "{}-12-15".format(GBQualifier_value_text)
else:
date_to_write = "{}-01-15".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 = parse(GBQualifier_value_text).strftime('%Y-%m-%d')
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'
if GBQualifier_value_text in term_to_uri_dict:
GBQualifier_value_text = term_to_uri_dict[GBQualifier_value_text]
else:
missing_value_list.append('\t'.join([accession_version, GBQualifier_name_text, GBQualifier_value_text]))
info_for_yaml_dict['sample']['collection_location'] = GBQualifier_value_text
elif GBQualifier_name_text == 'note':
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':
info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+GBQualifier_value_text.split('taxon:')[1]
# Remove technology key if empty!
if (info_for_yaml_dict['technology']=={}):
del info_for_yaml_dict['technology']
with open(os.path.join(dir_fasta_and_yaml, '{}.fasta'.format(accession_version)), 'w') as fw:
fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper()))
with open(os.path.join(dir_fasta_and_yaml, '{}.yaml'.format(accession_version)), 'w') as fw:
json.dump(info_for_yaml_dict, fw, indent=2)
if(len(GBSeq_sequence.text) >= min_len_to_count):
num_seq_with_len_ge_X_bp += 1
if len(missing_value_list) > 0:
with open('missing_terms.tsv', 'w') as fw:
fw.write('\n'.join(missing_value_list))
print('Num. sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp))
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