genbank: pseudo workflow

1 files changed, 326 insertions, 0 deletions

diff --git a/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py b/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
new file mode 100755
index 0000000..8b970b6
--- /dev/null
+++ b/workflows/pull-data/genbank/transform-genbank-xml2yamlfa.py
@@ -0,0 +1,326 @@
+#!/usr/bin/env python3
+#
+# Create a single YAML/FASTA from genbank XML
+
+# ----------------------------------------------------------------------
+"""
+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))