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数据与复现
PO
Polars
维护者 K-Dense Inc. · 最近更新 2026年4月1日
Polars：polars-bio是一个high-performance Python 库 ，用于 genomic interval operations 、 bioinformatics file I/O，built on Polars，Apache Arrow，、 Apache DataFusion。 It provides familiar DataFrame-centric API ，用于 interval arithmetic (overlap，nearest，merge，coverage，complement，subtract) 、 reading/writing common bioinformatics formats (BED，VCF，BAM，CRAM，GFF/GTF，FASTA，FASTQ)。
原始来源
K-Dense-AI/claude-scientific-skills
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/polars-bio
- 维护者
- K-Dense Inc.
- 许可
- https://github.com/biodatageeks/polars-bio/blob/main/LICENSE
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- 6-38x faster than bioframe on real-world genomic 基准评测。
- Streaming/out-of-core support ，用于 large genomes ，通过 DataFusion。
- Cloud-native file I/O (S3，GCS，Azure) ，支持 predicate pushdown。
- Two API styles：functional (pb.overlap(df1，df2)) 、 method-chaining (df1.lazy().pb.overlap(df2))。
- SQL interface ，用于 genomic data ，通过 DataFusion SQL engine。
原始文档
SKILL.md 摘录
When to Use This Skill
Use this skill when:
- Performing genomic interval operations (overlap, nearest, merge, coverage, complement, subtract)
- Reading/writing bioinformatics file formats (BED, VCF, BAM, CRAM, GFF/GTF, FASTA, FASTQ)
- Processing large genomic datasets that don't fit in memory (streaming mode)
- Running SQL queries on genomic data files
- Migrating from bioframe to a faster alternative
- Computing read depth/pileup from BAM/CRAM files
- Working with Polars DataFrames containing genomic intervals
Basic Overlap Example
import polars as pl
import polars_bio as pb
## Create two interval DataFrames
df1 = pl.DataFrame({
"chrom": ["chr1", "chr1", "chr1"],
"start": [1, 5, 22],
"end": [6, 9, 30],
})
df2 = pl.DataFrame({
"chrom": ["chr1", "chr1"],
"start": [3, 25],
"end": [8, 28],
})
适用场景
- Performing genomic interval operations (overlap，nearest，merge，coverage，complement，subtract)。
- Reading/writing bioinformatics file formats (BED，VCF，BAM，CRAM，GFF/GTF，FASTA，FASTQ)。
- Processing large genomic 数据集s that don't fit in memory (streaming mode)。
- Running SQL queries on genomic data files。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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