1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
|
#!/usr/bin/env python3
from Bio import Entrez
Entrez.email = 'another_email@gmail.com'
import xml.etree.ElementTree as ET
import json
import os
from datetime import date
#today = date.today().strftime("%Y%m%d")
dir_metadata_today = 'metadata_from_nuccore' #_{}'.format(today)
dir_fasta_and_yaml_today = 'fasta_and_yaml' #'.format(today)
dir_dict_ontology_standardization = 'dict_ontology_standardization/'
path_ncbi_virus_accession = 'sequences.acc'
# Take all the ids
id_set = set()
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]
print(term, len(tmp_list))
tmp_list=tmp_list
# tmp_list = tmp_list[0:2] # restricting to small run
id_set.update([x.split('.')[0] for x in tmp_list])
print(term_list, len(id_set))
with open(path_ncbi_virus_accession) as f:
tmp_list = [line.strip('\n') for line in f]
print('NCBI Virus', len(tmp_list))
id_set.update(tmp_list)
print(term_list + ['NCBI Virus'], len(id_set))
def chunks(lst, n):
for i in range(0, len(lst), n):
yield lst[i:i + n]
num_ids_for_request = 100
if not os.path.exists(dir_metadata_today):
os.makedirs(dir_metadata_today)
for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)):
path_metadata_xxx_xml = os.path.join(dir_metadata_today, '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'
}
if not os.path.exists(dir_fasta_and_yaml_today):
os.makedirs(dir_fasta_and_yaml_today)
for path_metadata_xxx_xml in [os.path.join(dir_metadata_today, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata_today) 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
# 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'] = accession_version
info_for_yaml_dict['submitter']['authors'] = ';'.join([x.text for x in GBSeq.iter('GBAuthor')])
GBSeq_comment = GBSeq.find('GBSeq_comment')
if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text:
GBSeq_comment_text = GBSeq_comment.text.split('##Assembly-Data-START## ; ')[1].split(' ; ##Assembly-Data-END##')[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").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:
print(accession_version, 'missing technologies:', seq_tec)
new_seq_tec_list.append(seq_tec)
for n, seq_tec in enumerate(new_seq_tec_list):
info_for_yaml_dict['technology'][field_in_yaml + ('' if n == 0 else str(n + 1))] = seq_tec
else:
info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse
#term_to_uri_dict
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('; ')
#info_for_yaml_dict['host']['host_common_name'] = GBQualifier_value_text_list[0] # Removed
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]]
if len(GBQualifier_value_text_list) > 1:
if GBQualifier_value_text_list[1] in ['male', 'female']:
if GBQualifier_value_text_list[1]=='male':
info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384"
elif GBQualifier_value_text_list[1]=='female':
info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000383"
else:
info_for_yaml_dict['host']['host_health_status'] = GBQualifier_value_text_list[1]
if 'age' in GBQualifier_value_text:
info_for_yaml_dict['host']['host_age'] = int(GBQualifier_value_text_list[2].split('age ')[1])
info_for_yaml_dict['host']['host_age_unit'] = 'year'
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 in term_to_uri_dict:
info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict[GBQualifier_value_text]
else:
if GBQualifier_value_text in ['NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'np/np swab', 'np/op']:
info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal swab']
info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['oropharyngeal swab']
else:
print(accession_version, 'missing 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
elif GBQualifier_name_text in ['lat_lon', 'country']:
if GBQualifier_value_text in term_to_uri_dict:
GBQualifier_value_text = term_to_uri_dict[GBQualifier_value_text]
else:
print(accession_version, 'missing {}:'.format(GBQualifier_name_text), GBQualifier_value_text)
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
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_today, '{}.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_today, '{}.yaml'.format(accession_version)), 'w') as fw:
json.dump(info_for_yaml_dict, fw, indent=2)
|
