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polars-bio

High-performance genomic interval operations and bioinformatics file I/O on Polars DataFrames. Overlap, nearest, merge, coverage, complement, subtract for BED/VCF/BAM/GFF intervals. Streaming, cloud-native, faster bioframe alternative.

66

Quality

83%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

The canonical home for this skill is polars-bio in K-Dense-AI/scientific-agent-skills

SKILL.md
Quality
Evals
Security

Quality

Content

86%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

An exemplary API-reference skill body: executable examples, precise library-specific gotchas, and a clean one-level-deep reference structure with all pointers resolving to real files. The main improvement opportunity is tightening repetition — LazyFrame return semantics stated three times and a duplicated overlap example — and softening the unverifiable performance marketing claims.

DimensionReasoningScore

Conciseness

The body is dense with library-specific facts Claude cannot know (probe/build ordering, INT32 position limit, .pb accessor availability on LazyFrame vs DataFrame, coordinate metadata propagation) and avoids explaining generic concepts. However, the LazyFrame-return behavior is stated three times (Quick Start, section 1 intro, and the Key Concepts 'Return Types' section), the overlap example is duplicated between Quick Start and section 1, and the '6-38x faster' value-proposition bullets read as marketing padding — minor instances that could be trimmed, matching the 4 anchor rather than 5.

4 / 5

Actionability

Code examples are copy-paste ready with imports, real data, exact parameter names (suffixes, cols1/cols2, output_type, min_mapping_quality, use_zero_based), exact option keys, exact exception names (MissingCoordinateSystemError, CoordinateSystemMismatchError), and a concrete remediation command (samtools index) for a missing BAM index. This matches the 'fully executable; copy-paste ready' anchor and covers the common cases across interval ops, file I/O, SQL, and pileup.

5 / 5

Workflow Clarity

The document is well sequenced (install → quick start → capabilities → key concepts → pitfalls → best practices) and the Common Pitfalls section functions as error-recovery guidance (e.g., enabling coordinate_system_check to raise instead of warn, required .bai index, probe/build ordering). No destructive or batch operations apply, so the validation cap does not bind, but there are no explicit validate→fix→retry checkpoints either — clear sequence with mostly implicit checkpoints matches the 4 anchor rather than 5.

4 / 5

Progressive Disclosure

The body is a genuine overview: each capability section ends with an inline 'Reference: See references/<file>.md' pointer, the Resources section describes all six reference files, every referenced file exists in the bundle, and references are one level deep. This matches the 'clear overview with well-signaled one-level-deep references; content appropriately split' anchor.

5 / 5

Total

18

/

20

Passed

Description

75%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A highly specific, distinctive description that names concrete operations, formats, and performance characteristics in third person without padding. Its one structural weakness is the absence of an explicit 'Use when...' trigger clause, which both caps completeness and leaves natural trigger phrases like 'intersect' and FASTA/FASTQ/CRAM unused.

Suggestions

Append an explicit trigger clause such as 'Use when performing genomic interval arithmetic (intersect/overlap/merge), reading or writing BED/VCF/BAM/CRAM/GFF/FASTA/FASTQ files, or migrating from bioframe' to raise completeness from 3 to 5.

Include the common synonym 'intersect' alongside 'overlap' and mention the FASTA/FASTQ/CRAM formats so users searching with those natural terms match the description.

Consider trimming the marketing-flavored 'Streaming, cloud-native, faster bioframe alternative' tail to a factual clause, since 'faster' is an unverifiable over-claim unless tied to the benchmark reference.

DimensionReasoningScore

Specificity

The description lists six concrete interval operations ('Overlap, nearest, merge, coverage, complement, subtract'), names the target formats (BED/VCF/BAM/GFF), and states I/O plus streaming/cloud capabilities — comprehensive concrete actions with no vague filler. This matches the 'lists multiple specific concrete actions; comprehensive coverage' anchor rather than 4, since coverage of the library's core operations is complete rather than having minor gaps.

5 / 5

Completeness

The 'what' is explicit and concrete (interval operations and file I/O on Polars DataFrames), but there is no 'Use when...' clause or equivalent explicit trigger guidance; 'faster bioframe alternative' only weakly implies a migration use case. Per the judging guideline, a missing 'Use when...' clause caps completeness at 3 — clear what, when only weakly implied.

3 / 5

Trigger Term Quality

Natural keywords users would say are present ('overlap', 'merge', 'coverage', 'genomic interval', 'BED', 'VCF', 'bioframe', 'Polars'), but common variations are missing: 'intersect' (the standard synonym for overlap), FASTA/FASTQ/CRAM formats, and file extensions like .bed/.vcf. Good coverage with a few natural terms missing matches the 4 anchor rather than 5, and is well above the 'some relevant keywords but missing variations' level 3.

4 / 5

Distinctiveness Conflict Risk

The niche is clear and distinctive (genomic interval operations on Polars DataFrames, explicit bioframe alternative), with trigger terms unlikely to fire for unrelated skills. This matches the 'clear niche with distinct triggers; minimal conflict risk' anchor.

5 / 5

Total

17

/

20

Passed

Validation

93%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

15

/

16

Passed

Repository
synthetic-sciences/openscience
Reviewed

Table of Contents

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