Merge branch 'master' into patch-3

1 files changed, 193 insertions, 156 deletions

diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 0c410d7..f76cb29 100644..100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -1,59 +1,59 @@
+#!/usr/bin/env python3
+
 from Bio import Entrez
-Entrez.email = 'insert_your_email@gmail.com'
+Entrez.email = 'another_email@gmail.com'
 
 import xml.etree.ElementTree as ET
-import yaml
+import json
 import os
 
-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)
+num_ids_for_request = 100
 
+dir_metadata = 'metadata_from_nuccore'
+dir_fasta_and_yaml = 'fasta_and_yaml'
 dir_dict_ontology_standardization = 'dict_ontology_standardization/'
-
 path_ncbi_virus_accession = 'sequences.acc'
 
-# Take all the ids
-id_set = set()
+def chunks(lst, n):
+    for i in range(0, len(lst), n):
+        yield lst[i:i + n]
 
-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']
+if not os.path.exists(dir_metadata):
+    os.makedirs(dir_metadata)
 
-    # 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']]
+    # Take all the ids
+    id_set = set()
 
-    # Remove the version in the id
-    tmp_list = [x.split('.')[0] for x in tmp_list]
-    
-    print(term, len(tmp_list))
+    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']
 
-    id_set.update([x.split('.')[0] for x in 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']]
 
-print(term_list, len(id_set))
+        # Remove the version in the id
+        tmp_list = [x.split('.')[0] for x in tmp_list]
 
-with open(path_ncbi_virus_accession) as f:
-    tmp_list = [line.strip('\n') for line in f]
+        print(term, len(tmp_list))
+        tmp_list=tmp_list
+    #    tmp_list = tmp_list[0:2] # restricting to small run
 
-print('NCBI Virus', len(tmp_list))
-id_set.update(tmp_list)
+        id_set.update([x.split('.')[0] for x in tmp_list])
 
-print(term_list + ['NCBI Virus'], len(id_set))
+    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))
 
-def chunks(lst, n):
-    for i in range(0, len(lst), n):
-        yield lst[i:i + n]
-        
-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))
+        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:
@@ -61,7 +61,7 @@ if not os.path.exists(dir_metadata_today):
                 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')]:
@@ -72,144 +72,181 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x
             if len(line.split(',')) > 2:
                 term, uri = line.strip('\n').split('",')
                 term = term.strip('"')
-            else:    
+            else:
                 term, uri = line.strip('\n').split(',')
 
             term_to_uri_dict[term] = uri
 
 species_to_taxid_dict = {
-    'Homo sapiens': 9606
+    'Homo sapiens': 'http://purl.obolibrary.org/obo/NCBITaxon_9606'
 }
 
 
-if not os.path.exists(dir_fasta_and_yaml_today):
-    os.makedirs(dir_fasta_and_yaml_today)
+if not os.path.exists(dir_fasta_and_yaml):
+    os.makedirs(dir_fasta_and_yaml)
 
-    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()
+missing_value_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
+
+
+        # 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'] = 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!
+                        try:
+                            info_for_yaml_dict['technology'][field_in_yaml] = float(
+                                tech_info_to_parse.strip('(average)').strip("reads/nt").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:
+                                #print(accession_version, 'missing sample_sequencing_technology:', seq_tec)
+                                missing_value_list.append('\t'.join([accession_version, 'sample_sequencing_technology', seq_tec]))
 
-        for GBSeq in GBSet:
-            accession_version = GBSeq.find('GBSeq_accession-version').text
+                            new_seq_tec_list.append(seq_tec)
 
-            GBSeq_sequence = GBSeq.find('GBSeq_sequence')
-            if GBSeq_sequence is None:
-                print(accession_version, ' - sequence not found')
-                continue
+                        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
 
 
-            # 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
 
-                        
-                        #term_to_uri_dict
+        for GBFeature in GBSeq.iter('GBFeature'):
+            if GBFeature.find('GBFeature_key').text != 'source':
+                continue
 
-            for GBFeature in GBSeq.iter('GBFeature'):
-                if GBFeature.find('GBFeature_key').text != 'source':
+            for GBQualifier in GBFeature.iter('GBQualifier'):
+                GBQualifier_value = GBQualifier.find('GBQualifier_value')
+                if GBQualifier_value is None:
                     continue
+                GBQualifier_value_text = GBQualifier_value.text
 
-                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
+                GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text
 
-                    if GBQualifier_name_text == 'host':
-                        GBQualifier_value_text_list = GBQualifier_value_text.split('; ')
+                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]
+                    #info_for_yaml_dict['host']['host_common_name'] = GBQualifier_value_text_list[0] # Removed
 
-                        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 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
+                    if len(GBQualifier_value_text_list) > 1:
+                        if GBQualifier_value_text_list[1] in ['male', 'female']:
+                            if GBQualifier_value_text_list[1]=='male':
+                                info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384"
+                            elif GBQualifier_value_text_list[1]=='female':
+                                info_for_yaml_dict['host']['host_sex'] = "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:
-                            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]
+                            #print(accession_version, 'missing {}:'.format(GBQualifier_name_text), GBQualifier_value_text_list[1])
+                            missing_value_list.append('\t'.join([accession_version, GBQualifier_name_text, 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.upper() in term_to_uri_dict:
+                        GBQualifier_value_text = GBQualifier_value_text.upper() # For example, in case of 'usa: wa'
+                    
+                    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', 'np/op']:
+                            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']
+                        elif GBQualifier_value_text in ['nasopharyngeal swab/throat 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['throat swab']
+                        elif GBQualifier_value_text in ['nasopharyngeal aspirate/throat swab']:
+                            info_for_yaml_dict['sample']['specimen_source'] = term_to_uri_dict['nasopharyngeal aspirate']
+                            info_for_yaml_dict['sample']['specimen_source2'] = term_to_uri_dict['throat swab']
                         else:
-                            if GBQualifier_value_text in ['NP/OP swab', 'nasopharyngeal and oropharyngeal swab', 'nasopharyngeal/oropharyngeal swab', 'np/np swab', 'np/op']:
-                                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)
+                            #print(accession_version, 'missing specimen_source:', GBQualifier_value_text)
+                            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?
+                    info_for_yaml_dict['sample']['collection_date'] = GBQualifier_value_text
+                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:
+                        GBQualifier_value_text = term_to_uri_dict[GBQualifier_value_text]
+                    else:
+                        #print(accession_version, 'missing {}:'.format(GBQualifier_name_text), GBQualifier_value_text)
+                        missing_value_list.append('\t'.join([accession_version, 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'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+GBQualifier_value_text.split('taxon:')[1]
+
+
+        # Remove technology key if empty!
+        if (info_for_yaml_dict['technology']=={}):
+            del info_for_yaml_dict['technology']
+
+        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(missing_value_list) > 0:
+    with open('missing_terms.tsv', 'w') as fw:
+        fw.write('\n'.join(missing_value_list))