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change 'MAPPED TRAIT' and 'MAPPED TRAIT URI' to match published studies #162

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Jan 10, 2024
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change 'MAPPED TRAIT' and 'MAPPED TRAIT URI' to match published studies #162

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12 changes: 6 additions & 6 deletions dataExport/unpublish_study_export.py
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Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,7 @@ def build_studies_download(url, outputdir):
with open(outputdir + '/gwas-catalog-unpublished-studies-v1.0.3.tmp.tsv', 'w', newline='') as csvfile:
fieldnames = ['DATE ADDED TO CATALOG', 'PUBMED ID', 'FIRST AUTHOR', 'DATE', 'JOURNAL', 'LINK', 'STUDY',
'DISEASE/TRAIT', 'INITIAL SAMPLE SIZE', 'REPLICATION SAMPLE SIZE',
'PLATFORM [SNPS PASSING QC]', 'ASSOCIATION COUNT', 'MAPPED TRAIT', 'MAPPED TRAIT URI',
'PLATFORM [SNPS PASSING QC]', 'ASSOCIATION COUNT', 'MAPPED_TRAIT', 'MAPPED_TRAIT_URI',
'STUDY ACCESSION', 'GENOTYPING TECHNOLOGY', 'SUMMARY STATS LOCATION', 'SUBMISSION DATE',
'STATISTICAL MODEL', 'BACKGROUND TRAIT', 'MAPPED BACKGROUND TRAIT',
'MAPPED BACKGROUND TRAIT URI']
Expand All @@ -124,8 +124,8 @@ def build_studies_download(url, outputdir):
table['REPLICATION SAMPLE SIZE'] = 'not yet curated'
table['PLATFORM [SNPS PASSING QC]'] = (study['array_manufacturer'] or 'NR') + ' [' + str(study['variant_count'] or 'NR') + ']'
table['ASSOCIATION COUNT'] = 'not yet curated'
table['MAPPED TRAIT'] = 'not yet curated'
table['MAPPED TRAIT URI'] = 'not yet curated'
table['MAPPED_TRAIT'] = 'not yet curated'
table['MAPPED_TRAIT_URI'] = 'not yet curated'
table['STUDY ACCESSION'] = study['study_accession']
table['GENOTYPING TECHNOLOGY'] = study['genotyping_technology']
table['SUMMARY STATS LOCATION'] = generate_sumstats_ftp_path(study['study_accession'])
Expand All @@ -150,7 +150,7 @@ def build_studies_download_new(url, outputdir):
with open(outputdir + '/gwas-catalog-unpublished-studies-v1.0.3.1.tmp.tsv', 'w', newline='') as csvfile:
fieldnames = ['DATE ADDED TO CATALOG', 'PUBMED ID', 'FIRST AUTHOR', 'DATE', 'JOURNAL', 'LINK', 'STUDY',
'DISEASE/TRAIT', 'INITIAL SAMPLE SIZE', 'REPLICATION SAMPLE SIZE',
'PLATFORM [SNPS PASSING QC]', 'ASSOCIATION COUNT', 'MAPPED TRAIT', 'MAPPED TRAIT URI',
'PLATFORM [SNPS PASSING QC]', 'ASSOCIATION COUNT', 'MAPPED_TRAIT', 'MAPPED_TRAIT_URI',
'STUDY ACCESSION', 'GENOTYPING TECHNOLOGY', 'SUBMISSION DATE',
'STATISTICAL MODEL', 'BACKGROUND TRAIT', 'MAPPED BACKGROUND TRAIT','MAPPED BACKGROUND TRAIT URI',
'COHORT', 'FULL SUMMARY STATISTICS', 'SUMMARY STATS LOCATION']
Expand All @@ -166,8 +166,8 @@ def build_studies_download_new(url, outputdir):
table['REPLICATION SAMPLE SIZE'] = 'not yet curated'
table['PLATFORM [SNPS PASSING QC]'] = (study['array_manufacturer'] or 'NR') + ' [' + str(study['variant_count'] or 'NR') + ']'
table['ASSOCIATION COUNT'] = 'not yet curated'
table['MAPPED TRAIT'] = 'not yet curated'
table['MAPPED TRAIT URI'] = 'not yet curated'
table['MAPPED_TRAIT'] = 'not yet curated'
table['MAPPED_TRAIT_URI'] = 'not yet curated'
table['STUDY ACCESSION'] = study['study_accession']
table['GENOTYPING TECHNOLOGY'] = study['genotyping_technology']
table['SUBMISSION DATE'] = datetime.date.fromtimestamp(study['createdDate'] / 1000).isoformat()
Expand Down