Rename script/from_genbank_to_fasta_and_yaml.py to scripts/from_genbank_to_fasta_and_yaml.py

1 files changed, 141 insertions, 0 deletions

diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
new file mode 100644
index 0000000..0cc1a57
--- /dev/null
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -0,0 +1,141 @@
+from Bio import Entrez
+Entrez.email = 'your_email_to_be_polite'
+
+import xml.etree.ElementTree as ET
+import yaml
+import os
+
+path_ncbi_virus_accession = 'sequences.acc'
+
+date = '20200414'
+path_seq_fasta = 'seq_from_nuccore.{}.fasta'.format(date)
+path_metadata_xml = 'metadata_from_nuccore.{}.xml'.format(date)
+
+# Take all the ids
+id_set = set()
+
+term_list = ['SARS-CoV-2', 'SARS-CoV2', 'SARS CoV2', 'SARSCoV2', 'txid2697049[Organism]']
+for term in term_list:
+    tmp_list = Entrez.read(
+        Entrez.esearch(db='nuccore', term=term, idtype='acc', retmax='10000')
+    )['IdList']
+    print(term, len(tmp_list))
+    
+    # Remove the version in the id
+    id_set.update([x.split('.')[0] for x in tmp_list])
+
+print(term_list, len(id_set))
+
+with open(path_ncbi_virus_accession) as f:
+    tmp_list = [line.strip('\n') for line in f]
+
+print('NCBI Virus', len(tmp_list))
+id_set.update(tmp_list)
+
+print(term_list + ['NCBI Virus'], len(id_set))
+
+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()
+        )
+        
+        
+tree = ET.parse(path_metadata_xml)
+GBSet = tree.getroot()
+
+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
+
+
+    # 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:
+                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:
+                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)