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authorAndreaGuarracino2020-06-22 23:29:35 +0200
committerAndreaGuarracino2020-06-22 23:29:35 +0200
commit640675e07505dc0f7969480fe0643653e6408ec2 (patch)
treeae1bfcbfb4cf9d2b911df5f84f5f13a165876af6 /scripts
parent75ad6744aa8edb7de92a427c55405d9331879ad4 (diff)
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added new script to prepare metadata of sra data
Diffstat (limited to 'scripts')
-rw-r--r--scripts/download_sra_data/SraExperimentPackage.2020.06.08.xml.gzbin0 -> 3227724 bytes
-rw-r--r--scripts/download_sra_data/download_sra_data.py232
2 files changed, 232 insertions, 0 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
new file mode 100644
index 0000000..f9cd995
--- /dev/null
+++ b/scripts/download_sra_data/SraExperimentPackage.2020.06.08.xml.gz
Binary files differ
diff --git a/scripts/download_sra_data/download_sra_data.py b/scripts/download_sra_data/download_sra_data.py
new file mode 100644
index 0000000..9145a43
--- /dev/null
+++ b/scripts/download_sra_data/download_sra_data.py
@@ -0,0 +1,232 @@
+#!/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