new script release

- now the script is more gentle with the server, requesting metadata in batches, reducing the ovrall execution time;
- in the YAML files are created field for sample_sequencing_technology, sample_sequencing_technology2, sample_sequencing_technology3, specimen_source, and specimen_source2;
- in sequencing_coverage stuff like 'x', 'X', etc... is stripped, and the ',' replaced by '.';
- the script exploits the dictionaries in the /scripts/dict_ontology_standardization. Now I have used ncbi_specesman_source.csv, ncbi_sequencing_technology.csv, and ncbi_countries.csv.
- in ncbi_sequencing_technology.csv I've added 'Oxford Nanopore' and 'MinION Oxford Nanopore'
- for  specimen_source, when there is one of 'NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', or 'np/np swab', I put both of them.

1 files changed, 170 insertions, 100 deletions

diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 0cc1a57..a7c9dc2 100644
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -1,15 +1,19 @@
 from Bio import Entrez
-Entrez.email = 'your_email_to_be_polite'
+Entrez.email = 'andresguarahino@gmail.com'
 
 import xml.etree.ElementTree as ET
 import yaml
 import os
 
-path_ncbi_virus_accession = 'sequences.acc'
+from datetime import date
+today = date.today().strftime("%Y%m%d")
+
+dir_metadata_today = 'metadata_from_nuccore_{}'.format(today)
+dir_fasta_and_yaml_today = 'fasta_and_yaml_{}'.format(today)
 
-date = '20200414'
-path_seq_fasta = 'seq_from_nuccore.{}.fasta'.format(date)
-path_metadata_xml = 'metadata_from_nuccore.{}.xml'.format(date)
+dir_dict_ontology_standardization = 'dict_ontology_standardization/'
+
+path_ncbi_virus_accession = 'sequences.acc'
 
 # Take all the ids
 id_set = set()
@@ -19,9 +23,15 @@ for term in term_list:
     tmp_list = Entrez.read(
         Entrez.esearch(db='nuccore', term=term, idtype='acc', retmax='10000')
     )['IdList']
-    print(term, len(tmp_list))
-    
+
+    # Remove mRNAs, ncRNAs, Proteins, and predicted models (more information here: https://en.wikipedia.org/wiki/RefSeq)
+    tmp_list = [x for x in tmp_list if x[:2] not in ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP']]
+
     # Remove the version in the id
+    tmp_list = [x.split('.')[0] for x in tmp_list]
+    
+    print(term, len(tmp_list))
+
     id_set.update([x.split('.')[0] for x in tmp_list])
 
 print(term_list, len(id_set))
@@ -34,108 +44,168 @@ id_set.update(tmp_list)
 
 print(term_list + ['NCBI Virus'], len(id_set))
 
-if not os.path.exists(path_metadata_xml):
-    # TO_DO: to check if I already have the records?
-    
-    with open(path_metadata_xml, 'w') as fw:
-        fw.write(
-            Entrez.efetch(db='nuccore', id=list(id_set), retmode='xml').read()
-        )
-        
+def chunks(lst, n):
+    for i in range(0, len(lst), n):
+        yield lst[i:i + n]
         
-tree = ET.parse(path_metadata_xml)
-GBSet = tree.getroot()
+num_ids_for_request = 100
+if not os.path.exists(dir_metadata_today):
+    os.makedirs(dir_metadata_today)
+    
+    for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)):
+        path_metadata_xxx_xml = os.path.join(dir_metadata_today, 'metadata_{}.xml'.format(i))
+        print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xml))
+
+        with open(path_metadata_xxx_xml, 'w') as fw:
+            fw.write(
+                Entrez.efetch(db='nuccore', id=id_x_list, retmode='xml').read()
+            )
+
+            
+term_to_uri_dict = {}
+
+for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_xxx_csv) for name_xxx_csv in os.listdir(dir_dict_ontology_standardization) if name_xxx_csv.endswith('.csv')]:
+    print('Read {}'.format(path_dict_xxx_csv))
+
+    with open(path_dict_xxx_csv) as f:
+        for line in f:
+            term, uri = line.strip('\n').split(',')
+
+            term_to_uri_dict[term] = uri
 
 species_to_taxid_dict = {
     'Homo sapiens': 9606
 }
 
-for GBSeq in GBSet:
-    accession_version = GBSeq.find('GBSeq_accession-version').text
-
-    GBSeq_sequence = GBSeq.find('GBSeq_sequence')
-    if GBSeq_sequence is None:
-        print(accession_version, ' - sequence not found')
-        continue
 
+if os.path.exists(dir_fasta_and_yaml_today):
+    os.makedirs(dir_fasta_and_yaml_today)
 
-    # A general default-empty yaml could be read from the definitive one
-    info_for_yaml_dict = {
-        'id': 'placeholder',
-        'host': {},
-        'sample': {},
-        'virus': {},
-        'technology': {},
-        'submitter': {}
-    }
-    
+    for path_metadata_xxx_xml in [os.path.join(dir_metadata_today, name_metadata_xxx_xml) for name_metadata_xxx_xml in os.listdir(dir_metadata_today) if name_metadata_xxx_xml.endswith('.xml')]:
+        tree = ET.parse(path_metadata_xxx_xml)
+        GBSet = tree.getroot()
 
-    info_for_yaml_dict['sample']['sample_id'] = accession_version
-    info_for_yaml_dict['submitter']['authors'] = ';'.join([x.text for x in GBSeq.iter('GBAuthor')])
+        for GBSeq in GBSet:
+            accession_version = GBSeq.find('GBSeq_accession-version').text
 
-    
-    GBSeq_comment = GBSeq.find('GBSeq_comment')
-    if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text:
-        GBSeq_comment_text = GBSeq_comment.text.split('##Assembly-Data-START## ; ')[1].split(' ; ##Assembly-Data-END##')[0]
-
-        for info_to_check, field_in_yaml in zip(
-            ['Assembly Method', 'Coverage', 'Sequencing Technology'],
-            ['sequence_assembly_method', 'sequencing_coverage', 'sample_sequencing_technology']
-        ):
-            if info_to_check in GBSeq_comment_text:
-                info_for_yaml_dict['technology'][field_in_yaml] = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0]
-    
-    
-    for GBFeature in GBSeq.iter('GBFeature'):
-        if GBFeature.find('GBFeature_key').text != 'source':
-            continue
-            
-        for GBQualifier in GBFeature.iter('GBQualifier'):
-            GBQualifier_value = GBQualifier.find('GBQualifier_value')
-            if GBQualifier_value is None:
+            GBSeq_sequence = GBSeq.find('GBSeq_sequence')
+            if GBSeq_sequence is None:
+                print(accession_version, ' - sequence not found')
                 continue
-            GBQualifier_value_text = GBQualifier_value.text
-
-            GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text
-
-            if GBQualifier_name_text == 'host':
-                GBQualifier_value_text_list = GBQualifier_value_text.split('; ')
-
-                info_for_yaml_dict['host']['host_common_name'] = GBQualifier_value_text_list[0]
-
-                if GBQualifier_value_text_list[0] in species_to_taxid_dict:
-                    info_for_yaml_dict['host']['host_species'] = species_to_taxid_dict[GBQualifier_value_text_list[0]]
-
-                if len(GBQualifier_value_text_list) > 1:
-                    if GBQualifier_value_text_list[1] in ['male', 'female']:
-                        info_for_yaml_dict['host']['host_sex'] = GBQualifier_value_text_list[1]
-                    else:
-                        info_for_yaml_dict['host']['host_health_status'] = GBQualifier_value_text_list[1]
-
-                    if 'age' in GBQualifier_value_text:
-                        info_for_yaml_dict['host']['host_age'] = int(GBQualifier_value_text_list[2].split('age ')[1])
-                        info_for_yaml_dict['host']['host_age_unit'] = 'year'
-            elif GBQualifier_name_text == 'collected_by':
-                if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]):
-                    info_for_yaml_dict['sample']['collecting_institution'] = GBQualifier_value_text
-                else:
-                    info_for_yaml_dict['sample']['collector_name'] = GBQualifier_value_text
-            elif GBQualifier_name_text == 'isolation_source':
-                info_for_yaml_dict['sample']['specimen_source'] = GBQualifier_value_text
-            elif GBQualifier_name_text == 'collection_date':
-                # TO_DO: which format we will use?
-                info_for_yaml_dict['sample']['collection_date'] = GBQualifier_value_text
-            elif GBQualifier_name_text in ['lat_lon', 'country']:
-                info_for_yaml_dict['sample']['collection_location'] = GBQualifier_value_text
-            elif GBQualifier_name_text == 'note':
-                info_for_yaml_dict['sample']['additional_collection_information'] = GBQualifier_value_text
-            elif GBQualifier_name_text == 'isolate':
-                info_for_yaml_dict['virus']['virus_strain'] = GBQualifier_value_text
-            elif GBQualifier_name_text == 'db_xref':
-                info_for_yaml_dict['virus']['virus_species'] = int(GBQualifier_value_text.split('taxon:')[1])
-    
-    with open('{}.fasta'.format(accession_version), 'w') as fw:
-        fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper()))
 
-    with open('{}.yaml'.format(accession_version), 'w') as fw:
-        yaml.dump(info_for_yaml_dict, fw, default_flow_style=False)
+
+            # A general default-empty yaml could be read from the definitive one
+            info_for_yaml_dict = {
+                'id': 'placeholder',
+                'host': {},
+                'sample': {},
+                'virus': {},
+                'technology': {},
+                'submitter': {}
+            }
+
+
+            info_for_yaml_dict['sample']['sample_id'] = accession_version
+            info_for_yaml_dict['submitter']['authors'] = ';'.join([x.text for x in GBSeq.iter('GBAuthor')])
+
+
+            GBSeq_comment = GBSeq.find('GBSeq_comment')
+            if GBSeq_comment is not None and 'Assembly-Data' in GBSeq_comment.text:
+                GBSeq_comment_text = GBSeq_comment.text.split('##Assembly-Data-START## ; ')[1].split(' ; ##Assembly-Data-END##')[0]
+
+                for info_to_check, field_in_yaml in zip(
+                    ['Assembly Method', 'Coverage', 'Sequencing Technology'],
+                    ['sequence_assembly_method', 'sequencing_coverage', 'sample_sequencing_technology']
+                ):
+                    if info_to_check in GBSeq_comment_text:
+                        tech_info_to_parse = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0]
+                        
+                        if field_in_yaml == 'sequencing_coverage':
+                            # A regular expression would be better!
+                            info_for_yaml_dict['technology'][field_in_yaml] = ';'.join(
+                                [x.strip('(average)').strip("reads/nt").replace(',', '.').strip(' xX>') for x in tech_info_to_parse.split(';')]
+                            )
+                        elif field_in_yaml == 'sample_sequencing_technology':
+                            new_seq_tec_list = []
+                            for seq_tec in tech_info_to_parse.split(';'):
+                                seq_tec = seq_tec.strip()
+                                if seq_tec in term_to_uri_dict:
+                                    seq_tec = term_to_uri_dict[seq_tec]
+                                else:
+                                    print(accession_version, 'missing technologies:', seq_tec)
+ 
+                                new_seq_tec_list.append(seq_tec)
+
+                            for n, seq_tec in enumerate(new_seq_tec_list):
+                                info_for_yaml_dict['technology'][field_in_yaml + ('' if n == 0 else str(n + 1))] = seq_tec
+                        else:
+                            info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse
+
+                        
+                        #term_to_uri_dict
+
+            for GBFeature in GBSeq.iter('GBFeature'):
+                if GBFeature.find('GBFeature_key').text != 'source':
+                    continue
+
+                for GBQualifier in GBFeature.iter('GBQualifier'):
+                    GBQualifier_value = GBQualifier.find('GBQualifier_value')
+                    if GBQualifier_value is None:
+                        continue
+                    GBQualifier_value_text = GBQualifier_value.text
+
+                    GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text
+
+                    if GBQualifier_name_text == 'host':
+                        GBQualifier_value_text_list = GBQualifier_value_text.split('; ')
+
+                        info_for_yaml_dict['host']['host_common_name'] = GBQualifier_value_text_list[0]
+
+                        if GBQualifier_value_text_list[0] in species_to_taxid_dict:
+                            info_for_yaml_dict['host']['host_species'] = species_to_taxid_dict[GBQualifier_value_text_list[0]]
+
+                        if len(GBQualifier_value_text_list) > 1:
+                            if GBQualifier_value_text_list[1] in ['male', 'female']:
+                                info_for_yaml_dict['host']['host_sex'] = GBQualifier_value_text_list[1]
+                            else:
+                                info_for_yaml_dict['host']['host_health_status'] = GBQualifier_value_text_list[1]
+
+                            if 'age' in GBQualifier_value_text:
+                                info_for_yaml_dict['host']['host_age'] = int(GBQualifier_value_text_list[2].split('age ')[1])
+                                info_for_yaml_dict['host']['host_age_unit'] = 'year'
+                    elif GBQualifier_name_text == 'collected_by':
+                        if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]):
+                            info_for_yaml_dict['sample']['collecting_institution'] = GBQualifier_value_text
+                        else:
+                            info_for_yaml_dict['sample']['collector_name'] = GBQualifier_value_text
+                    elif GBQualifier_name_text == 'isolation_source':
+                        if GBQualifier_value_text in term_to_uri_dict:
+                            info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict[GBQualifier_value_text]
+                        else:
+                            if GBQualifier_value_text in ['NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'np/np swab']:
+                                info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal swab']
+                                info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['oropharyngeal swab']
+                            else:
+                                print(accession_version, 'missing specimen_source:', GBQualifier_value_text)
+                    elif GBQualifier_name_text == 'collection_date':
+                        # TO_DO: which format we will use?
+                        info_for_yaml_dict['sample']['collection_date'] = GBQualifier_value_text
+                    elif GBQualifier_name_text in ['lat_lon', 'country']:
+                        if GBQualifier_value_text in term_to_uri_dict:
+                            GBQualifier_value_text = term_to_uri_dict[GBQualifier_value_text]
+                        else:
+                            print(accession_version, 'missing {}:'.format(GBQualifier_name_text), GBQualifier_value_text)
+
+                        info_for_yaml_dict['sample']['collection_location'] = GBQualifier_value_text
+                    elif GBQualifier_name_text == 'note':
+                        info_for_yaml_dict['sample']['additional_collection_information'] = GBQualifier_value_text
+                    elif GBQualifier_name_text == 'isolate':
+                        info_for_yaml_dict['virus']['virus_strain'] = GBQualifier_value_text
+                    elif GBQualifier_name_text == 'db_xref':
+                        info_for_yaml_dict['virus']['virus_species'] = int(GBQualifier_value_text.split('taxon:')[1])
+
+            with open(os.path.join(dir_fasta_and_yaml_today, '{}.fasta'.format(accession_version)), 'w') as fw:
+                fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper()))
+
+            with open(os.path.join(dir_fasta_and_yaml_today, '{}.yaml'.format(accession_version)), 'w') as fw:
+                yaml.dump(info_for_yaml_dict, fw, default_flow_style=False)