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-rw-r--r--scripts/download_sra_data/download_sra_data.py45
1 files changed, 28 insertions, 17 deletions
diff --git a/scripts/download_sra_data/download_sra_data.py b/scripts/download_sra_data/download_sra_data.py
index 9145a43..e36afb6 100644
--- a/scripts/download_sra_data/download_sra_data.py
+++ b/scripts/download_sra_data/download_sra_data.py
@@ -8,9 +8,11 @@ import gzip
dir_yaml = 'yaml'
-date = '2020.06.08'
+date = '2020.07.05'
-# Query on SRA: 'txid2697049[Organism]' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism%5D) -> Send to -> File -> Full XML -> Create File
+# 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/'
@@ -70,14 +72,14 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
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
+ #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')
@@ -100,11 +102,19 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
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
+ 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']:
+ 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_text
+ 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]]
@@ -179,17 +189,18 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
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']
@@ -197,7 +208,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
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']
+ info_for_yaml_dict['submitter']['publication'] = STUDY.attrib['alias']
Organization = EXPERIMENT_PACKAGE.find('Organization')
@@ -229,4 +240,4 @@ 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
+ fw.write('\n'.join(missing_value_list))