moved the genbank script in his specific directory

1 files changed, 0 insertions, 395 deletions

diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
deleted file mode 100755
index 6216340..0000000
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ /dev/null
@@ -1,395 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-parser = argparse.ArgumentParser()
-parser.add_argument('--skip-request', action='store_true', help='skip metadata and sequence request', required=False)
-parser.add_argument('--only-missing-id', action='store_true', help='download only missing id', required=False)
-args = parser.parse_args()
-
-from Bio import Entrez
-Entrez.email = 'another_email@gmail.com'
-
-import xml.etree.ElementTree as ET
-import json
-import os
-import requests
-import sys
-
-from datetime import date
-from dateutil.parser import parse
-
-num_ids_for_request = 100
-
-dir_metadata = 'metadata_from_nuccore'
-dir_fasta_and_yaml = 'fasta_and_yaml'
-dir_dict_ontology_standardization = 'dict_ontology_standardization/'
-
-today_date = date.today().strftime("%Y.%m.%d")
-path_ncbi_virus_accession = 'sequences.{}.acc'.format(today_date)
-
-def is_integer(string_to_check):
-    try:
-        int(string_to_check)
-        return True
-    except ValueError:
-        return False
-
-def chunks(lst, n):
-    for i in range(0, len(lst), n):
-        yield lst[i:i + n]
-
-if os.path.exists(dir_metadata):
-    print("The directory '{}' already exists.".format(dir_metadata))
-
-    if not args.skip_request:
-        print("\tTo start the request, delete the directory '{}' or specify --skip-request.".format(dir_metadata))
-        sys.exit(-1)
-
-
-accession_already_downloaded_set = []
-
-if os.path.exists(dir_fasta_and_yaml):
-    print("The directory '{}' already exists.".format(dir_fasta_and_yaml))
-    if not args.only_missing_id:
-        print("To start the download, delete the directory '{}' or specify --only-missing-id.".format(dir_fasta_and_yaml))
-        sys.exit(-1)
-
-    accession_already_downloaded_set = set([x.split('.yaml')[0].split('.')[0] for x in os.listdir(dir_fasta_and_yaml) if x.endswith('.yaml')])
-    print('There are {} accession already downloaded.'.format(len(accession_already_downloaded_set)))
-
-
-if not os.path.exists(dir_metadata):
-    # Take all the ids
-    id_set = set()
-
-    # Try to search several strings
-    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']
-
-        # 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]
-
-        #tmp_list = tmp_list[0:2] # restricting to small run
-        new_ids_set = set([x.split('.')[0] for x in tmp_list])
-        new_ids = len(new_ids_set.difference(id_set))
-        id_set.update(new_ids_set)
-
-        print('Term:', term, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set))
-
-    if not os.path.exists(path_ncbi_virus_accession):
-        r = requests.get('https://www.ncbi.nlm.nih.gov/genomes/VirusVariation/vvsearch2/?q=*:*&fq=%7B!tag=SeqType_s%7DSeqType_s:(%22Nucleotide%22)&fq=VirusLineageId_ss:(2697049)&cmd=download&sort=SourceDB_s%20desc,CreateDate_dt%20desc,id%20asc&dlfmt=acc&fl=id')
-        with open(path_ncbi_virus_accession, 'w') as fw:
-            fw.write(r.text)
-
-    with open(path_ncbi_virus_accession) as f:
-        tmp_list = [line.strip('\n') for line in f]
-
-    new_ids = len(set(tmp_list).difference(id_set))
-    id_set.update(tmp_list)
-
-    print('DB: NCBI Virus', today_date, '-->', new_ids, 'new IDs from', len(tmp_list), '---> Total unique IDs:', len(id_set))
-
-    if len(accession_already_downloaded_set) > 0:
-        id_set = id_set.difference(accession_already_downloaded_set)
-        print('There are {} missing IDs to download.'.format(len(id_set)))
-
-    os.makedirs(dir_metadata)
-    for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)):
-        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:
-            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:
-            if len(line.split(',')) > 2:
-                term, uri = line.strip('\n').split('",')
-                term = term.strip('"')
-            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
-
-if not os.path.exists(dir_fasta_and_yaml):
-    os.makedirs(dir_fasta_and_yaml)
-
-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)
-    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:
-                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]))
-
-                                new_seq_tec_list.append(seq_tec)
-
-                            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_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:
-                            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', 'combined nasopharyngeal and 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.lower() in ['nasopharyngeal swab/throat swab', 'nasopharyngeal/throat swab', 'nasopharyngeal swab and throat swab', 'nasal swab and throat swab', 'nasopharyngeal aspirate/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.lower() in ['nasal swab and throat swab']:
-                                info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['throat swab']]
-                            elif GBQualifier_value_text.lower() in ['nasal-swab and oro-pharyngeal swab']:
-                                info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict['nasal swab'], term_to_uri_dict['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 += '-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_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]
-
-
-            # 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(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:
-    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))