Examples¶

Copy-pasteable commands for common tasks. Screenshots are TBD.

1. Everything for a project (data + metadata)¶

adaptiseq -i PRJNA211801

Resolves every Run in the project, downloads each through the segmented engine, and md5-verifies it.

2. Metadata only¶

adaptiseq -i PRJNA211801 -m
adaptiseq -i CRR343031 -m

→ PRJNA211801.metadata.tsv (and for GSA, *.metadata.csv + CRA*.metadata.xlsx).

3. Direct gzip FASTQ¶

adaptiseq -i SRR1178105 -g

4. Convert SRA → FASTQ (single-cell friendly)¶

adaptiseq -i SRR1178105 -q -t 10

5. Batch download a list, in parallel¶

adaptiseq -i accessions.txt -g            # adaptive worker pool (default)
adaptiseq -i accessions.txt -g -j 8 --no-adaptive   # fixed 8 workers

accessions.txt — one accession per line, databases may be mixed:

SRR7706354
PRJNA480016
CRR311377
GSM7417667

6. Merge an Experiment's Runs¶

adaptiseq -i SRX003906 -g -e ex

7. Aspera (ENA), adaptive pool¶

adaptiseq -i ena_list.txt -a --aspera-efficiency 0.8

8. Force a database / protocol¶

adaptiseq -i SRR1178105 -d sra
adaptiseq -i SRR7706354 -g -r https

9. From Python¶

from adaptiseq import fetch, get_metadata

rows   = get_metadata("SRR7706354")
result = fetch("accessions.txt", outdir="data/", gzip=True, jobs=20, adaptive=True)
print(result.success_ids, result.fail_ids, result.failed)

10. Resume an interrupted run¶

Just re-run the same command. Completed Runs in success.log are skipped, and partially downloaded files (*.part/*.part.meta) are resumed, not restarted. To force a re-download of one Run:

sed -i '/SRR7706354/d' success.log
adaptiseq -i SRR7706354 -g