genbank: moving script into workflow space

3 files changed, 498 insertions, 0 deletions

diff --git a/workflows/pull-data/genbank/.gitignore b/workflows/pull-data/genbank/.gitignore
new file mode 100644
index 0000000..69b8a57
--- /dev/null
+++ b/workflows/pull-data/genbank/.gitignore
@@ -0,0 +1,3 @@
+fasta_and_yaml/
+*.tsv
+*.acc
diff --git a/workflows/pull-data/genbank/.guix-run b/workflows/pull-data/genbank/.guix-run
new file mode 100644
index 0000000..1403c69
--- /dev/null
+++ b/workflows/pull-data/genbank/.guix-run
@@ -0,0 +1,5 @@
+#!/bin/sh
+# Runner
+
+echo python3 from_genbank_to_fasta_and_yaml.py
+guix environment guix --ad-hoc python python-biopython python-requests python-dateutil
diff --git a/workflows/pull-data/genbank/from_genbank_to_fasta_and_yaml.py b/workflows/pull-data/genbank/from_genbank_to_fasta_and_yaml.py
new file mode 100755
index 0000000..9b2c9eb
--- /dev/null
+++ b/workflows/pull-data/genbank/from_genbank_to_fasta_and_yaml.py
@@ -0,0 +1,490 @@
+#!/usr/bin/env python3
+#
+# - bulk download genbank data and matadata, preparing the FASTA and
+#   the YAML files
+#
+# See .guix-run python3 from_genbank_to_fasta_and_yaml.py
+
+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('--skip-request', action='store_true', help='skip metadata and sequence request', required=False)
+parser.add_argument('--only-missing-ids', action='store_true', help='download only missing ids not already downloaded', required=False)
+parser.add_argument('--dict-ontology', type=str, help='where is the ontology',
+                    default='../dict_ontology_standardization/', required=False)
+args = parser.parse_args()
+
+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, datetime
+from dateutil.parser import parse
+
+import sys
+sys.path.append('../')
+from utils import is_integer, chunks, check_and_get_ontology_dictionaries
+
+
+num_ids_for_request = 100
+min_acceptable_collection_date = datetime(2019, 12, 1)
+
+dir_metadata = 'metadata_from_nuccore'
+dir_fasta_and_yaml = 'fasta_and_yaml'
+dir_dict_ontology_standardization = args.dict_ontology
+
+today_date = date.today().strftime("%Y.%m.%d")
+path_ncbi_virus_accession = 'sequences.{}.acc'.format(today_date)
+
+
+field_to_term_to_uri_dict = check_and_get_ontology_dictionaries(dir_dict_ontology_standardization)
+
+
+if os.path.exists(dir_metadata):
+    print("The directory '{}' already exists.".format(dir_metadata))
+
+    if not args.skip_request:
+        print("\tTo start the request, delete the directory '{}' or specify --skip-request.".format(dir_metadata))
+        sys.exit(-1)
+
+
+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)))
+
+
+# ----------------------------------------------------------------------
+"""
+With --only-missing-ids only download accessions that we do not yet have!
+"""
+accession_already_downloaded_set = set()
+
+if os.path.exists(dir_fasta_and_yaml):
+    """
+    If the fasta_and_yaml directory exists and --only-missing-ids was set
+    we make a list of all downloaded accessions:
+    """
+    print("The directory '{}' already exists.".format(dir_fasta_and_yaml))
+    if not args.only_missing_ids:
+        print("To start the download, delete the directory '{}' or specify --only-missing-ids.".format(dir_fasta_and_yaml))
+        sys.exit(-1)
+
+    """
+    Fetch all YAML filenames and load `accession_already_downloaded_set`
+    """
+    accession_already_downloaded_set = set([x.split('.yaml')[0].split('.')[0] for x in os.listdir(dir_fasta_and_yaml) if x.endswith('.yaml')])
+    print('There are {} accessions already downloaded.'.format(len(accession_already_downloaded_set)))
+
+accession_to_ignore_set.update(accession_already_downloaded_set)
+
+# ----------------------------------------------------------------------
+"""
+Check for --ids-to-consider
+"""
+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)))
+
+# ----------------------------------------------------------------------
+"""
+Download section for genbank XML
+"""
+
+if not os.path.exists(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)
+        # Remove the version in the id
+        new_ids_set = set([x.split('.')[0] for x in tmp_list if x[:2] not in ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP']])
+
+        if len(accession_to_consider_set) > 0:
+            new_ids_set = new_ids_set.intersection(accession_to_consider_set)
+
+        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_set = set(tmp_list)
+    if len(accession_to_consider_set) > 0:
+        new_ids_set = new_ids_set.intersection(accession_to_consider_set)
+
+    new_ids = len(new_ids_set.difference(id_set))
+    id_set.update(new_ids_set)
+
+    print('DB: NCBI Virus', today_date, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set))
+
+    id_set = id_set.difference(accession_to_ignore_set)
+    print('There are {} missing IDs to download.'.format(len(id_set)))
+
+    os.makedirs(dir_metadata)
+    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()
+            )
+
+# ----------------------------------------------------------------------
+"""
+Generate metadata (YAML) and FASTA files for each accession
+"""
+
+
+if not os.path.exists(dir_fasta_and_yaml):
+    os.makedirs(dir_fasta_and_yaml)
+
+min_len_to_count = 15000
+num_seq_with_len_ge_X_bp = 0
+
+missing_value_list = []
+not_created_accession_dict = {}
+accession_with_errors_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
+
+        try:
+            # 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:
+                author_list = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')]
+                if len(author_list) > 0:
+                    info_for_yaml_dict['submitter']['authors'] = author_list
+
+                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
+
+            # This script download and prepare data and metadata for assemblies samples
+            info_for_yaml_dict['technology']['assembly_method'] = 'http://purl.obolibrary.org/obo/GENEPIO_0001628'
+
+            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'],
+                    ['alignment_protocol', '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.replace('(average)', '').replace("reads/nt", '').
+                                          replace('(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 field_to_term_to_uri_dict['ncbi_sequencing_technology']:
+                                    seq_tec = field_to_term_to_uri_dict['ncbi_sequencing_technology'][seq_tec]
+                                    new_seq_tec_list.append(seq_tec)
+                                else:
+                                    missing_value_list.append('\t'.join([accession_version, 'sample_sequencing_technology', seq_tec]))
+
+                            if len(new_seq_tec_list) > 0:
+                                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 = GBQualifier_value_text.split(';')[0] # For case like Homo sapiens;sex:female
+                        if GBQualifier_value_text in field_to_term_to_uri_dict['ncbi_host_species']:
+                            # Cases like 'Felis catus; Domestic Shorthair'
+                            info_for_yaml_dict['host']['host_species'] = field_to_term_to_uri_dict['ncbi_host_species'][GBQualifier_value_text]
+                        else:
+                            GBQualifier_value_text_list = GBQualifier_value_text.split('; ')
+
+                            if GBQualifier_value_text_list[0] 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'][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'] = field_to_term_to_uri_dict['ncbi_host_species']['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 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'][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 >= 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 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 field_to_term_to_uri_dict['ncbi_speciesman_source']:
+                            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 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'][GBQualifier_value_text]]
+                        else:
+                            if GBQualifier_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 GBQualifier_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 GBQualifier_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 GBQualifier_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 GBQualifier_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']]
+                            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 = parse(GBQualifier_value_text).strftime('%Y-%m') + '-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_name_text == 'country' and ': ' in GBQualifier_value_text:
+                            GBQualifier_value_text = GBQualifier_value_text.replace(': ', ':')
+
+                        if GBQualifier_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'][GBQualifier_value_text]
+                        else:
+                            missing_value_list.append('\t'.join([accession_version, GBQualifier_name_text, 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]
+
+            # Check if mandatory fields are missing
+            if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']:
+                # print(accession_version, ' - technology not found')
+                if accession_version not in not_created_accession_dict:
+                    not_created_accession_dict[accession_version] = []
+                not_created_accession_dict[accession_version].append('sample_sequencing_technology not found')
+
+            if 'collection_location' not in info_for_yaml_dict['sample']:
+                if accession_version not in not_created_accession_dict:
+                    not_created_accession_dict[accession_version] = []
+                not_created_accession_dict[accession_version].append('collection_location not found')
+
+            if 'collection_date' not in info_for_yaml_dict['sample']:
+                if accession_version not in not_created_accession_dict:
+                    not_created_accession_dict[accession_version] = []
+                not_created_accession_dict[accession_version].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_version not in not_created_accession_dict:
+                        not_created_accession_dict[accession_version] = []
+                    not_created_accession_dict[accession_version].append('collection_date too early')
+
+            if 'authors' not in info_for_yaml_dict['submitter']:
+                if accession_version not in not_created_accession_dict:
+                    not_created_accession_dict[accession_version] = []
+                not_created_accession_dict[accession_version].append('authors not found')
+
+            if 'host_species' not in info_for_yaml_dict['host']:
+                if accession_version not in not_created_accession_dict:
+                    not_created_accession_dict[accession_version] = []
+                not_created_accession_dict[accession_version].append('host_species not found')
+
+            if len(GBSeq_sequence.text) < min_len_to_count:
+                if accession_version not in not_created_accession_dict:
+                    not_created_accession_dict[accession_version] = []
+                not_created_accession_dict[accession_version].append('sequence shorter than {} bp'.format(min_len_to_count))
+
+            if accession_version not in not_created_accession_dict:
+                num_seq_with_len_ge_X_bp += 1
+
+                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)
+        except:
+            print("Unexpected error for the ID {}: {}".format(accession_version, sys.exc_info()[0]))
+            accession_with_errors_list.append(accession_version)
+            continue
+
+if len(missing_value_list) > 0:
+    path_missing_terms_tsv = 'missing_terms.genbank.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(accession_with_errors_list) > 0:
+    path_accession_with_errors_tsv = 'accession_with_errors.genbank.tsv'
+    print('Written the accession with errors in {}'.format(path_accession_with_errors_tsv))
+    with open(path_accession_with_errors_tsv, 'w') as fw:
+        fw.write('\n'.join(accession_with_errors_list))
+
+if len(not_created_accession_dict) > 0:
+    path_not_created_accession_tsv = 'not_created_accession.genbank.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. new sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp))