GeoFetcheroo

GeoFetcheroo is a command‑line utility that bridges GEO/dbGAP and SRA to give you all the sequencing run details you need.

Additional Details

• One‑step workflow: From a GEO Series (GSE) to SRR runs and human‑readable sample names in a single script.
• No manual scraping: Automates FTP, HTML or CSV parsing by using R’s GEOquery and NCBI’s EDirect tools.
• Tab‑delimited output: Easy to import into spreadsheets, R/Python data frames or downstream pipelines.

Dependencies

• R (≥ 4.0)
• esearch

  sh -c "$(curl -fsSL https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"

• GEOquery R package

  install.packages("GEOquery")
  

Quick run

Clone the repo:

git clone https://github.com/jssprrt/GeoFetcheroo.git
cd GeoFetcheroo
chmod +x GeoFetcheroo.sh

Execute:

./GeoFetcheroo.sh GSE193201

Output:

Found GSM IDs: GSM5776310 GSM5776311 GSM5776312 GSM5776313 GSM5776314 GSM5776315 GSM5776322 GSM5776323 GSM5776324 GSM5776325 GSM5776326 GSM5776327 GSM5776328 GSM5776329 GSM5776330 GSM5776331 GSM5776332 GSM5776333 GSM5942920 GSM5942921 GSM5942922

Derived SRX IDs: SRX13652506 SRX13652507 SRX13652508 SRX13652509 SRX13652510 SRX13652511 SRX13652518 SRX13652519 SRX13652520 SRX13652521 SRX13652522 SRX13652523 SRX13652524 SRX13652525 SRX13652526 SRX13652527 SRX13652528 SRX13652529 SRX14421485 SRX14421486 SRX14421487

GSE	SRX	SRR	BioSample	BioSampleTitle
GSE193201	SRX13652506	SRR17482016	SAMN24719625	CFG2295 PM18_D28_5F_RNAseq
GSE193201	SRX13652507	SRR17482015	SAMN24719624	CFG2296 PM18_D28_5F-O_RNAseq
GSE193201	SRX13652508	SRR17482014	SAMN24719623	CFG2334 PM18_D28_5F-K_RNAseq
GSE193201	SRX13652509	SRR17482013	SAMN24719622	CFG2336 PM10_D28_5F_RNAseq
GSE193201	SRX13652510	SRR17482012	SAMN24719621	CFG2337 PM10_D28_5F-K_RNAseq
GSE193201	SRX13652511	SRR17482011	SAMN24719620	CFG2338 PM10_D28_5F-O_RNAseq
GSE193201	SRX13652518	SRR17482004	SAMN24719613	CFG2351 PM18_D28_5F_PEF_RRBS
GSE193201	SRX13652519	SRR17482003	SAMN24719612	CFG2352 PM18_D28_5F-O_PEF_RRBS
GSE193201	SRX13652520	SRR17482002	SAMN24719611	CFG2353 PM18_D28_5F-K_PEF_RRBS
GSE193201	SRX13652521	SRR17482001	SAMN24719610	CFG2354 PM10_D28_5F_PEF_RRBS
GSE193201	SRX13652522	SRR17482000	SAMN24719609	CFG2355 PM10_D28_5F-O_PEF_RRBS
GSE193201	SRX13652523	SRR17481999	SAMN24719608	CFG2356 PM10_D28_5F-K_PEF_RRBS
GSE193201	SRX13652524	SRR17481998	SAMN24719607	CFG2351-seq2 PM18_D28_5F_PEF_RRBS
GSE193201	SRX13652525	SRR17481997	SAMN24719606	CFG2352-seq2 PM18_D28_5F-O_PEF_RRBS
GSE193201	SRX13652526	SRR17481996	SAMN24719605	CFG2353-seq2 PM18_D28_5F-K_PEF_RRBS
GSE193201	SRX13652527	SRR17481995	SAMN24719604	CFG2354-seq2 PM10_D28_5F_PEF_RRBS
GSE193201	SRX13652528	SRR17481994	SAMN24719603	CFG2355-seq2 PM10_D28_5F-O_PEF_RRBS
GSE193201	SRX13652529	SRR17481993	SAMN24719602	CFG2356-seq2 PM10_D28_5F-K_PEF_RRBS
GSE193201	SRX14421485	SRR18283673	SAMN26545672	PM9_D28_5F_RNAseq
GSE193201	SRX14421486	SRR18283672	SAMN26545671	PM9_D28_5F-O_RNAseq
GSE193201	SRX14421487	SRR18283671	SAMN26545670	PM9_D28_5F-K_RNAseq

Running for dbGAP:

./GeoFetcheroo.sh --dbgap phs001431