feat(cli): add geo-matrix command to download and convert GEO matrix files to TSV #233
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📋 Description
Added a new CLI command
geo-matrix-to-tsv
topysradb
for downloading and converting GEO Series Matrix files (GSE
) to clean TSV format.This supports optional skipping of downloads if files already exist.
✅ Type of Change
ℹ️ Additional Information
🔧 Functionality:
pysradb geo-matrix-to-tsv GSE12345 --outdir ./output --skip-download
.txt
/.gz
matrix file from GEO FTP..tsv
format for downstream analysis.--outdir
.🧪 Testing:
GSE10072
,GSE60424
--skip-download
is set.📸 Screenshot/Logs
$ pysradb geo-matrix-to-tsv GSE10072 --outdir ./tsv_output ✔️ Download complete ✔️ Converted GSE10072_series_matrix.txt.gz → GSE10072_series_matrix.tsv
🔗 Link to Ticket
Fix for - #229