use GEOparse to download series supplemental files?
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Entering edit mode
11 weeks ago
mk ▴ 290

This GSE series has multiple supplemental files that are listed as Series_supplemental_file in the GSE163697_family.soft.gz and shown in the "Supplementary file" table you see with many GSE series on GEO and shown in the picture below:

enter image description here

However, it seems that GEOparse.GSE.download_supplementary_files() only looks for SRA metadata for the associated GSM files, and ignores series supplementary files mentioned above:

geo_accession = "GSE163697"
gse = GEOparse.GSE.get_GEO(geo=geo_accession, destdir=destination_directory)
gse.download_supplementary_files(
    download_sra=False,
    directory=destination_directory,
    email="me@gmail.com",
    sra_kwargs={'threads':32})

Is there any option to get series supplemental files as well?

gse geoparse python geoquery geo • 222 views
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