use polars to go from SRA accessions to run identifiers

[ctb]

Luiz shows us a nice command:

AllTheBacteria/AllTheBacteria#54 (comment)

[bluegenes]

I modified Luiz's script to get run accs from a bioproject, worked like a charm:

# /// script
# dependencies = [
#   "polars>=1.17.1,<2",
# ]
# ///

import polars as pl

sra_prj = "PRJEB74559"

sra_metadata = pl.scan_parquet(
    "s3://sra-pub-metadata-us-east-1/sra/metadata/",
    storage_options={"skip_signature": "true"},
).select(["acc", "bioproject"])

# Filter the SRA metadata for the specified Bioproject and write to a TSV file
sra_metadata.filter(pl.col("bioproject") == sra_prj).sink_csv(
    "PRJEB74559.accs.tsv", separator="\t"
)

saved as sra-project-to-runs.py
uv run sra-project-to-runs.py produces a file that looks like this:

acc     bioproject
ERR13485822     PRJEB74559
ERR13480653     PRJEB74559
ERR13480654     PRJEB74559
ERR13480650     PRJEB74559
ERR13488553     PRJEB74559
ERR13480663     PRJEB74559

🤩