Merge branch 'master' of https://github.com/arvados/bh20-seq-resource

2 files changed, 250 insertions, 0 deletions

diff --git a/scripts/create_sra_metadata/SraExperimentPackage.2020.07.05.xml.gz b/scripts/create_sra_metadata/SraExperimentPackage.2020.07.05.xml.gz
new file mode 100644
index 0000000..88acb18
--- /dev/null
+++ b/scripts/create_sra_metadata/SraExperimentPackage.2020.07.05.xml.gz
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py
new file mode 100644
index 0000000..ef0d119
--- /dev/null
+++ b/scripts/create_sra_metadata/create_sra_metadata.py
@@ -0,0 +1,250 @@
+#!/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 = '2020.07.05'
+
+# Query on SRA: 'txid2697049[Organism]' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism%5D)
+# Query on SRA: 'txid2697049[Organism:noexp] NOT 0[Mbases ' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism:noexp%5D%20NOT%200[Mbases)
+#         -> 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.lower() in ['homo sapien', 'homosapiens']:
+                    VALUE_text = 'Homo sapiens'
+
+                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', 'not provided']:
+                    value_to_insert = VALUE_text
+
+                    if value_to_insert.lower() in ['homo sapien', 'homosapiens']:
+                        value_to_insert = 'Homo sapiens'
+
+                    if value_to_insert in term_to_uri_dict:
+                        value_to_insert = term_to_uri_dict[value_to_insert]
+                        
+                    if 'virus_strain' not in info_for_yaml_dict:                        
+                        info_for_yaml_dict['virus']['virus_strain'] = value_to_insert
+                    else:
+                        info_for_yaml_dict['virus']['virus_strain'] += '; ' + value_to_insert
+            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]))
+    #else:
+    #    print(accession, 'Missing INSTRUMENT_MODEL', info_for_yaml_dict)
+    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'] = STUDY.attrib['alias']
+    
+    
+    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"
+
+    if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']:
+        print(accession, ' - technology not found')
+        continue
+
+    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))