polars-bio

Use this skill for genomic interval arithmetic and bioinformatics file I/O through Polars and DataFusion. It targets polars-bio 0.36.0, tested with Polars 1.44.2 on Python 3.13. The upstream package requires Polars >=1.37.1, PyArrow >=23.0.1,<25, DataFusion >=53,<54 and polars-config-meta >=0.3.2,<1. Keep this environment separate from packages needing incompatible Arrow or DataFusion releases.

uv pip install "polars-bio==0.36.0" "polars==1.44.2"
# Optional pandas interoperability (requires pandas >=3):
uv pip install "polars-bio[pandas]==0.36.0" "polars==1.44.2"

Verify new releases against the official release notes and package requirements. The examples below with named files are templates: substitute actual files and check their schemas. The synthetic interval example and small local format round trips were executed during this review.

Workflow

1. Record the assembly, contig naming, coordinate convention, strand policy and unit of analysis. Identical contig names do not prove identical assemblies.
2. Choose readers by format; BCF has its own reader. Inspect schemas and source metadata before selecting attributes or genotypes.
3. Normalize all inputs to one coordinate system and validate their bounds.
4. Choose pair output, hit counts, covered bases or read depth deliberately.
5. Filter and project lazily, then inspect a small result before scaling up.
6. Validate output counts and boundaries against a hand-computable fixture; preserve IDs, coordinate metadata and provenance when saving results.

Coordinate contract

The default is 1-based closed, including converted BED reads. Use use_zero_based=True on genomic readers for 0-based half-open output. This argument converts positions; it is not only a metadata label. For example, BED [0,10) becomes [1,10] by default and remains [0,10) with the override. SAM text POS is 1-based, whereas BAM stores its alignment position internally as 0-based. Both readers expose the requested output convention.

For manually constructed DataFrames, metadata labels existing numbers and does not convert them. Converting closed [s,e] to half-open means s-1,e. Set metadata only after conversion. Never convert twice.

import polars as pl
import polars_bio as pb

pb.set_option("datafusion.bio.coordinate_system_zero_based", True)
pb.set_option("datafusion.bio.coordinate_system_check", True)

query = pl.DataFrame({
    "query_id": ["q1", "q2", "q3"],
    "chrom": ["chr1", "chr1", "chr2"],
    "start": [0, 10, 0], "end": [10, 20, 10],
})
target = pl.DataFrame({
    "chrom": ["chr1", "chr1"], "start": [5, 8], "end": [12, 15],
})
for frame in (query, target):
    frame.config_meta.set(coordinate_system_zero_based=True)

pairs = pb.overlap(query, target).collect()
counts = pb.count_overlaps(query, target).collect().sort("query_id")
covered = pb.coverage(query, target).collect().sort("query_id")
assert pairs.height == 4
assert counts["count"].to_list() == [2, 2, 0]
assert covered["coverage"].to_list() == [5, 5, 0]

Require non-null contigs, integer positions and valid positive-length intervals (0 <= start < end in half-open form), within the chosen assembly. Do not silently turn points/insertions into nonempty intervals: choose the biological convention. Mismatched input metadata raises CoordinateSystemMismatchError; missing metadata warns and uses the global setting by default, or raises MissingCoordinateSystemError in strict mode. Inspect pb.get_metadata(frame) after transformations and SQL. See configuration.

Choose the operation

Important 0.36.0 behavior:

• on_cols is exposed in several signatures but not implemented; non-None values raise AssertionError. For strand/sample-specific analysis, split both inputs by that key, run matching groups separately and restore the group key.
• merge(..., min_dist=0) and cluster(..., min_dist=0) keep bookended half-open intervals separate. min_dist=1 joins bookends for integer coordinates. Test boundary fixtures when porting bioframe code; its threshold conventions differ.
• nearest supports k, overlap=False and distance=False. Distance zero can mean overlap or adjacency; it does not prove an intersecting base. Do not infer a unique biological annotation from an arbitrary equidistant candidate.
• Default COITrees overlap indexing casts coordinates to signed Int32; an Int64 DataFrame does not remove the 2,147,483,647 bound. Validate maximum coordinates before execution, especially concatenated genomes or custom coordinate spaces.
• complement without a view uses an effectively unbounded contig extent. Always supply finite genome bounds and ensure their convention matches the intervals.

Functional interval calls return pl.LazyFrame by default; .collect() or output_type="polars.DataFrame" gives an eager result. The .pb interval accessor is on LazyFrame: query.lazy().pb.overlap(target).collect(). DataFrame .pb provides write methods. See interval operations.

Read, query and write files

Use scan_* for lazy plans and read_* for eager reads. They do not guarantee that every stage, join index or final result fits in bounded memory.

# Template: both files use the same assembly; coordinates become half-open.
peaks = pb.scan_bed("peaks.bed", use_zero_based=True)
variants = pb.scan_vcf("cohort.vcf.gz", use_zero_based=True,
                       info_fields=[], format_fields=[])
hits = pb.overlap(peaks, variants).collect(engine="streaming")

Check these format-specific differences before analysis:

• read_bed/scan_bed expose BED4 fields. BED3 produces a null name; BED6/12 extra fields are not retained. Use scan_table(..., schema="bed6") or Polars CSV with an explicit schema for strand/block fields, then attach coordinate metadata.
• Text VCF uses read_vcf/scan_vcf; binary BCF uses read_bcf/scan_bcf. INFO defaults to header-defined columns, not a raw info string. Single-sample FORMAT is flattened; multisample FORMAT is a genotypes struct of lists.
• GFF/GTF attributes is structured. Request actual annotation keys using attr_fields, then filter named columns. FASTQ calls its quality string quality_scores, not quality.
• BAM/CRAM can scan without an index; indexes enable selective/parallel reads. read_cram/scan_cram accept a local reference_path with .fai when an external reference is needed. register_cram and depth lack that argument and require a self-contained reference arrangement.
• Native writers/sinks exist for VCF, BAM, SAM, CRAM, FASTA and FASTQ. Preserve format headers and metadata across transformations; writing only selected coordinate columns is not a valid full-format round trip.

See file I/O for current schemas, compression, cloud credentials, output fidelity and the local-only VCF Zarr reader.

SQL registration uses path first, table name second. register_fasta exists in 0.36.0. from_polars(name, frame) registers Polars data; register_view(name, sql) takes SQL text. pb.sql(query) returns a LazyFrame. Explicitly set the session coordinate convention before registering genomic files, and reattach confirmed coordinate metadata after SQL if it is absent. The 0.36.0 SQL interval-join optimizer has dtype and unmatched-row defects; use the tested interval APIs instead of assuming SQL LEFT JOIN semantics. See SQL.

Read depth is a separate measurement

pb.depth("sample.bam", use_zero_based=True) returns run-length blocks; per_base=True emits positions when contig lengths support dense accumulation. M, = and X contribute coverage; D and N do not. Default flag mask 1796 excludes unmapped, secondary, QC-failed and duplicate reads, but not supplementary reads. There is no base-quality threshold or fragment-count option in this API.

Depth is emitted as Int16. In 0.36.0, 32,768 reads covering one base wrap to -32,768; casting the result afterward cannot recover it. Do not use this function for ultra-deep data without an independent depth implementation. Use length-weighted block summaries and include zero-depth target bases in the denominator. See pileup operations for a tested summary pattern.

Scaling and reproducibility

Keep query/target order biologically correct: swapping inputs changes counts, coverage, nearest and subtraction. The second input is indexed for many joins, but default count_overlaps internally swaps operands. Benchmark the actual operation instead of following a universal larger-first rule.

Lazy scans can push supported filters/projections into readers; BED and FASTA do not offer the same pushdown as indexed VCF/BAM. collect(engine="streaming") still materializes the final DataFrame. Use sinks for large outputs, and budget memory for the build index, sorting, aggregation and dense pileup arrays. Start with the default single DataFusion partition and tune a small fixed number against measured throughput and memory. Record versions, options, assemblies, input checksums, filtering rules, row counts and interval coverage totals.

Cloud reads use format-specific OpenDAL options, not a universal Polars storage_options dictionary. Only request authenticated/provider-specific features for the relevant URI; cloud access was documentation-reviewed, while a small public HTTPS BED scan was executed. No authenticated S3/GCS/Azure service was tested. Report this distinction when troubleshooting.

See bioframe migration for semantic checks; polars-bio is not a drop-in replacement. Upstream benchmark speedups are specific to datasets, hardware and operations, not a performance promise.