Merge branch 'master' of https://github.com/arvados/bh20-seq-resource

2 files changed, 227 insertions, 214 deletions

diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv
new file mode 100644
index 0000000..0d2120c
--- /dev/null
+++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv
@@ -0,0 +1,6 @@
+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
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 65adb00..87e99d4 100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -123,18 +123,12 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x
             else:
                 term, uri = line.strip('\n').split(',')
 
+            if term in term_to_uri_dict:
+                print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term))
+                continue
+                
             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)
 
@@ -142,6 +136,7 @@ min_len_to_count = 27500
 num_seq_with_len_ge_X_bp = 0
 
 missing_value_list = []
+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)
@@ -155,232 +150,244 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
             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]))
+        try:
+            #print(path_metadata_xxx_xml, accession_version)
 
-                            new_seq_tec_list.append(seq_tec)
+            # 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['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
 
+            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
 
-        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']]
+            # 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:
-                            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)
+                            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:
-                            date_to_write = "{}-01-15".format(GBQualifier_value_text)
+                            info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse
 
-                        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)
+
+            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 term_to_uri_dict:
+                            info_for_yaml_dict['host']['host_species'] = term_to_uri_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'] = term_to_uri_dict['Canis lupus familiaris']
                         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)
+                            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']['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('-')
+                            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'
 
-                        if GBQualifier_value_text_list[1].isalpha():
-                            date_to_write = parse(GBQualifier_value_text).strftime('%Y-%m-%d')
+                        # Little cleaning
+                        GBQualifier_value_text = GBQualifier_value_text.strip("/'")
 
-                    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:
+                            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 GBQualifier_value_text in term_to_uri_dict:
-                        info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[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]
+                            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('-')
 
-        # Remove technology key if empty!
-        if (info_for_yaml_dict['technology']=={}):
-            del info_for_yaml_dict['technology']
+                            if GBQualifier_value_text_list[1].isalpha():
+                                date_to_write = parse(GBQualifier_value_text).strftime('%Y-%m-%d')
 
-        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()))
+                        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:
+                            info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[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]
 
-        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)
 
+            # Remove technology key if empty!
+            if (info_for_yaml_dict['technology']=={}):
+                del info_for_yaml_dict['technology']
 
-        if(len(GBSeq_sequence.text) >= min_len_to_count):
-        	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)
+
+
+            if(len(GBSeq_sequence.text) >= min_len_to_count):
+                num_seq_with_len_ge_X_bp += 1
+        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:
-    with open('missing_terms.tsv', 'w') as fw:
+    path_missing_terms_tsv = 'missing_terms.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.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))
+        
 print('Num. new sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp))