Merge pull request #90 from AndreaGuarracino/patch-21

genbank and sra scripts update, new terms in the ontology dictionaries

2 files changed, 0 insertions, 232 deletions

diff --git a/scripts/download_sra_data/SraExperimentPackage.2020.06.08.xml.gz b/scripts/download_sra_data/SraExperimentPackage.2020.06.08.xml.gz
deleted file mode 100644
index f9cd995..0000000
--- a/scripts/download_sra_data/SraExperimentPackage.2020.06.08.xml.gz
+++ /dev/null
diff --git a/scripts/download_sra_data/download_sra_data.py b/scripts/download_sra_data/download_sra_data.py
deleted file mode 100644
index 9145a43..0000000
--- a/scripts/download_sra_data/download_sra_data.py
+++ /dev/null
@@ -1,232 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-from dateutil.parser import parse
-import xml.etree.ElementTree as ET
-import json
-import gzip
-
-dir_yaml = 'yaml'
-
-date = '2020.06.08'
-
-# Query on SRA: 'txid2697049[Organism]' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism%5D) -> Send to -> File -> Full XML -> Create File
-path_sra_metadata_xml = 'SraExperimentPackage.{}.xml.gz'.format(date)
-
-dir_dict_ontology_standardization = '../dict_ontology_standardization/'
-path_sra_study_accessions_txt = 'SRAStudyAccessions.{}.txt'.format(date)
-
-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, 'r') 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(',')
-
-            term_to_uri_dict[term] = uri
-
-def is_integer(string_to_check):
-    try:
-        int(string_to_check)
-        return True
-    except ValueError:
-        return False
-
-if not os.path.exists(dir_yaml):
-    os.makedirs(dir_yaml)
-
-sra_metadata_xml_file = gzip.open(path_sra_metadata_xml, 'r')
-tree = ET.parse(sra_metadata_xml_file)
-sra_metadata_xml_file.close()
-
-EXPERIMENT_PACKAGE_SET = tree.getroot()
-
-missing_value_list = []
-
-run_accession_set = set()
-run_accession_to_downloadble_file_url_dict = {}
-
-for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
-    #print(i, EXPERIMENT_PACKAGE)
-    
-    # A general default-empty yaml could be read from the definitive one
-    info_for_yaml_dict = {
-        'id': 'placeholder',
-        'host': {},
-        'sample': {},
-        'virus': {},
-        'technology': {},
-        'submitter': {}
-    }
-
-    RUN_SET = EXPERIMENT_PACKAGE.find('RUN_SET')
-    RUN = RUN_SET.find('RUN')
-    accession = RUN.attrib['accession']
-    run_accession_set.add(accession)
-    #print(accession)
-    
-    info_for_yaml_dict['sample']['sample_id'] = accession
-    
-    SRAFiles = RUN.find('SRAFiles')
-    if SRAFiles is not None:
-        url = SRAFiles.find('SRAFile').attrib['url']
-        if 'sra-download.ncbi.nlm.nih.gov' in url:
-            run_accession_to_downloadble_file_url_dict[accession] = url
-  
-
-    SAMPLE = EXPERIMENT_PACKAGE.find('SAMPLE')
-    SAMPLE_ATTRIBUTE_list = SAMPLE.iter('SAMPLE_ATTRIBUTE')
-    
-    for SAMPLE_ATTRIBUTE in SAMPLE_ATTRIBUTE_list:
-        VALUE = SAMPLE_ATTRIBUTE.find('VALUE')
-        if VALUE is not None:
-            TAG_text = SAMPLE_ATTRIBUTE.find('TAG').text
-            VALUE_text = VALUE.text
-
-            if TAG_text in ['host', 'host scientific name']:
-                if VALUE_text in term_to_uri_dict:
-                    info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[VALUE_text]
-                else:
-                    missing_value_list.append('\t'.join([accession, 'host_species', VALUE_text]))
-            elif TAG_text in ['host_health_status', 'host health state']:
-                if VALUE_text in term_to_uri_dict:
-                    info_for_yaml_dict['host']['host_health_status'] = term_to_uri_dict[VALUE_text]                            
-                elif VALUE_text.strip("'") not in ['missing', 'not collected', 'not provided']:
-                    missing_value_list.append('\t'.join([accession, 'host_health_status', VALUE_text]))
-            elif TAG_text in ['strain', 'isolate']:
-                if VALUE_text.lower() not in ['not applicable', 'missing', 'na', 'unknown']:
-                    if 'virus_strain' not in info_for_yaml_dict:
-                        info_for_yaml_dict['virus']['virus_strain'] = VALUE_text
-                    else:
-                        info_for_yaml_dict['virus']['virus_strain'] += '; ' + VALUE_text
-            elif TAG_text in ['isolation_source', 'isolation source host-associated']:                    
-                if VALUE_text in term_to_uri_dict:
-                    info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[VALUE_text]]
-                else:
-                    if 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 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 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 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']]
-                    elif VALUE_text.strip("'") not in ['missing', 'not collected', 'unknown', 'not provided', 'not applicable', 'N/A']:
-                        missing_value_list.append('\t'.join([accession, 'specimen_source', VALUE_text]))
-            elif TAG_text in ['host_sex', 'host sex']:
-                if VALUE_text.lower() not in ['missing', 'not provided']:
-                    if VALUE_text in ['male', 'female']:
-                        info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" if VALUE_text == 'male' else "http://purl.obolibrary.org/obo/PATO_0000383"
-                    else:
-                        missing_value_list.append('\t'.join([accession, 'host_sex', VALUE_text]))
-            elif TAG_text in ['host_age', 'host age']:
-                if is_integer(VALUE_text):
-                    info_for_yaml_dict['host']['host_age'] = VALUE_text
-                    info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036'
-            elif TAG_text == 'collected_by':
-                if VALUE_text.lower() not in ['not available', 'missing']:
-                    name = VALUE_text in ['Dr. Susie Bartlett', 'Ahmed Babiker', 'Aisi Fu', 'Brandi Williamson', 'George Taiaroa', 'Natacha Ogando', 'Tim Dalebout', 'ykut Ozdarendeli']
-                    
-                    info_for_yaml_dict['sample']['collector_name' if name else 'collecting_institution'] = VALUE_text
-            elif TAG_text == 'collecting institution':
-                if VALUE_text.lower() not in ['not provided', 'na']:
-                    info_for_yaml_dict['sample']['collecting_institution'] = VALUE_text
-            elif TAG_text in ['collection_date', 'collection date']:
-                if VALUE_text.lower() not in ['not applicable', 'missing', 'na']:
-                    date_to_write = VALUE_text
-                    date_is_estimated = True
-                    
-                    VALUE_text_list = VALUE_text.split('-')
-                    if len(VALUE_text_list) == 3:
-                        date_is_estimated = False
-                        
-                        if VALUE_text_list[1].isalpha():
-                            date_to_write = parse(VALUE_text).strftime('%Y-%m-%d')
-                    elif len(VALUE_text_list) == 2:
-                        date_to_write =  VALUE_text + '-15'
-                    else:
-                        if int(VALUE_text) < 2020:
-                            date_to_write = "{}-12-15".format(VALUE_text)
-                        else:
-                            date_to_write = "{}-01-15".format(VALUE_text)
-
-                    info_for_yaml_dict['sample']['collection_date'] = date_to_write
-                    
-                    if date_is_estimated:
-                        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(VALUE_text)
-                        else:
-                            info_for_yaml_dict['sample']['additional_collection_information'] = "The 'collection_date' is estimated (the original date was: {})".format(VALUE_text)
-            elif TAG_text == 'geo_loc_name':
-                if VALUE_text in term_to_uri_dict:
-                    info_for_yaml_dict['sample']['collection_location'] = term_to_uri_dict[VALUE_text]
-                elif VALUE_text.lower() not in ['na', 'not applicable']:
-                    missing_value_list.append('\t'.join([accession, 'geo_loc_name', VALUE_text]))
-            #else:
-            #    if TAG_text not in ['lat_lon', 'host_disease', 'BioSampleModel', 'passage_history']:
-            #        print(accession, TAG_text, VALUE_text)
-
-
-    taxon_id = SAMPLE.find('SAMPLE_NAME').find('TAXON_ID').text
-    info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+taxon_id
-    
-    
-    EXPERIMENT = EXPERIMENT_PACKAGE.find('EXPERIMENT')
-    INSTRUMENT_MODEL = [x.text for x in EXPERIMENT.find('PLATFORM').iter('INSTRUMENT_MODEL')][0]
-    if INSTRUMENT_MODEL.lower() != 'unspecified':
-        if INSTRUMENT_MODEL in term_to_uri_dict:
-            info_for_yaml_dict['technology']['sample_sequencing_technology'] = [term_to_uri_dict[INSTRUMENT_MODEL]]
-        else:
-            missing_value_list.append('\t'.join([accession, 'sample_sequencing_technology', INSTRUMENT_MODEL]))
-    
-    LIBRARY_DESCRIPTOR = EXPERIMENT.find('DESIGN').find('LIBRARY_DESCRIPTOR')
-    if LIBRARY_DESCRIPTOR.text not in ['OTHER']:
-        info_for_yaml_dict['technology']['additional_technology_information'] = 'LIBRARY_STRATEGY: {};'.format(LIBRARY_DESCRIPTOR.find('LIBRARY_STRATEGY').text)
-           
-            
-    SUBMISSION = EXPERIMENT_PACKAGE.find('SUBMISSION')
-    info_for_yaml_dict['submitter']['submitter_sample_id'] = SUBMISSION.attrib['accession']
-    
-    if SUBMISSION.attrib['lab_name'].lower() not in ['na']:
-        info_for_yaml_dict['submitter']['originating_lab'] = SUBMISSION.attrib['lab_name']
-
-    STUDY = EXPERIMENT_PACKAGE.find('STUDY')     
-    info_for_yaml_dict['submitter']['publication'] = SUBMISSION.attrib['lab_name']
-    
-    
-    Organization = EXPERIMENT_PACKAGE.find('Organization')
-    Organization_Name = Organization.find('Name')
-    info_for_yaml_dict['submitter']['authors'] = [Organization_Name.text]
-        
-    Organization_Contact = Organization.find('Contact')
-    if Organization_Contact is not None:
-        Organization_Contact_Name = Organization_Contact.find('Name')
-        info_for_yaml_dict['submitter']['submitter_name'] = [Organization_Contact_Name.find('First').text + ' ' + Organization_Contact_Name.find('Last').text]
-        info_for_yaml_dict['submitter']['additional_submitter_information'] = Organization_Contact.attrib['email']
-
-        Organization_Concact_Address = Organization_Contact.find('Address')
-        if Organization_Concact_Address is not None:
-            info_for_yaml_dict['submitter']['submitter_address'] = '; '.join([x.text for x in Organization_Concact_Address] + ['Postal code ' + Organization_Concact_Address.attrib['postal_code']])
-
-    Organization_Address = Organization.find('Address')
-    if Organization_Address is not None:
-        info_for_yaml_dict['submitter']['lab_address'] = '; '.join([x.text for x in Organization_Address] + ['Postal code ' + Organization_Address.attrib['postal_code']])
-    
-    if 'collection_date' not in info_for_yaml_dict['sample']:
-        info_for_yaml_dict['sample']['collection_date'] = '1970-01-01'
-        info_for_yaml_dict['sample']['additional_collection_information'] = "The real 'collection_date' is missing"
-
-    with open(os.path.join(dir_yaml, '{}.yaml'.format(accession)), 'w') as fw:
-        json.dump(info_for_yaml_dict, fw, indent=2)
-    
-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))
\ No newline at end of file