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authorAndrea Guarracino2020-04-18 22:15:01 +0200
committerGitHub2020-04-18 22:15:01 +0200
commit3bee6777fb4a61febbf1c22e62d71d933cfba4b0 (patch)
treeedd1ae1b9c1080c2e9e28ec49df5fb8d38fe2144
parentbbca5ac9b2538e410efe3e09651f87e5573145de (diff)
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new script release
- now the script is more gentle with the server, requesting metadata in batches, reducing the ovrall execution time; - in the YAML files are created field for sample_sequencing_technology, sample_sequencing_technology2, sample_sequencing_technology3, specimen_source, and specimen_source2; - in sequencing_coverage stuff like 'x', 'X', etc... is stripped, and the ',' replaced by '.'; - the script exploits the dictionaries in the /scripts/dict_ontology_standardization. Now I have used ncbi_specesman_source.csv, ncbi_sequencing_technology.csv, and ncbi_countries.csv. - in ncbi_sequencing_technology.csv I've added 'Oxford Nanopore' and 'MinION Oxford Nanopore' - for specimen_source, when there is one of 'NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', or 'np/np swab', I put both of them.
-rw-r--r--scripts/from_genbank_to_fasta_and_yaml.py270
1 files changed, 170 insertions, 100 deletions
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 0cc1a57..a7c9dc2 100644
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -1,15 +1,19 @@
from Bio import Entrez
-Entrez.email = 'your_email_to_be_polite'
+Entrez.email = 'andresguarahino@gmail.com'
import xml.etree.ElementTree as ET
import yaml
import os
-path_ncbi_virus_accession = 'sequences.acc'
+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)
-date = '20200414'
-path_seq_fasta = 'seq_from_nuccore.{}.fasta'.format(date)
-path_metadata_xml = 'metadata_from_nuccore.{}.xml'.format(date)
+dir_dict_ontology_standardization = 'dict_ontology_standardization/'
+
+path_ncbi_virus_accession = 'sequences.acc'
# Take all the ids
id_set = set()
@@ -19,9 +23,15 @@ for term in term_list:
tmp_list = Entrez.read(
Entrez.esearch(db='nuccore', term=term, idtype='acc', retmax='10000')
)['IdList']
- print(term, len(tmp_list))
-
+
+ # 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))
+
id_set.update([x.split('.')[0] for x in tmp_list])
print(term_list, len(id_set))
@@ -34,108 +44,168 @@ id_set.update(tmp_list)
print(term_list + ['NCBI Virus'], len(id_set))
-if not os.path.exists(path_metadata_xml):
- # TO_DO: to check if I already have the records?
-
- with open(path_metadata_xml, 'w') as fw:
- fw.write(
- Entrez.efetch(db='nuccore', id=list(id_set), retmode='xml').read()
- )
-
+def chunks(lst, n):
+ for i in range(0, len(lst), n):
+ yield lst[i:i + n]
-tree = ET.parse(path_metadata_xml)
-GBSet = tree.getroot()
+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_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:
+ term, uri = line.strip('\n').split(',')
+
+ term_to_uri_dict[term] = uri
species_to_taxid_dict = {
'Homo sapiens': 9606
}
-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
+if os.path.exists(dir_fasta_and_yaml_today):
+ os.makedirs(dir_fasta_and_yaml_today)
- # A general default-empty yaml could be read from the definitive one
- info_for_yaml_dict = {
- 'id': 'placeholder',
- 'host': {},
- 'sample': {},
- 'virus': {},
- 'technology': {},
- 'submitter': {}
- }
-
+ 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()
- info_for_yaml_dict['sample']['sample_id'] = accession_version
- info_for_yaml_dict['submitter']['authors'] = ';'.join([x.text for x in GBSeq.iter('GBAuthor')])
+ for GBSeq in GBSet:
+ accession_version = GBSeq.find('GBSeq_accession-version').text
-
- 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:
- info_for_yaml_dict['technology'][field_in_yaml] = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0]
-
-
- 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:
+ GBSeq_sequence = GBSeq.find('GBSeq_sequence')
+ if GBSeq_sequence is None:
+ print(accession_version, ' - sequence not found')
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]
-
- 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']:
- info_for_yaml_dict['host']['host_sex'] = GBQualifier_value_text_list[1]
- 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':
- info_for_yaml_dict['sample']['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']:
- 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'] = int(GBQualifier_value_text.split('taxon:')[1])
-
- with open('{}.fasta'.format(accession_version), 'w') as fw:
- fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper()))
- with open('{}.yaml'.format(accession_version), 'w') as fw:
- yaml.dump(info_for_yaml_dict, fw, default_flow_style=False)
+
+ # 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['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!
+ info_for_yaml_dict['technology'][field_in_yaml] = ';'.join(
+ [x.strip('(average)').strip("reads/nt").replace(',', '.').strip(' xX>') for x in tech_info_to_parse.split(';')]
+ )
+ 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]
+
+ 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']:
+ info_for_yaml_dict['host']['host_sex'] = GBQualifier_value_text_list[1]
+ 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']:
+ 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'] = int(GBQualifier_value_text.split('taxon:')[1])
+
+ 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:
+ yaml.dump(info_for_yaml_dict, fw, default_flow_style=False)