使用Rust重写的gumpy

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项目描述

grumpy - 使用Rust重写的 gumpy，以实现速度提升

它不实现相同的接口，而是基于相同的原理。

比gumpy快100倍以上

安装

pip install bio-grumpy

用法

import grumpy

# Parse a genbank file
ref = grumpy.Genome("some/path/to/a/genbank/file.gbk")

# Parse a VCF file, respecting filter fails with a MIN_DP of 3 reads to make a call
vcf = grumpy.VCFFile("some/path/to/a/vcf/file.vcf", False, 3)

# Apply the VCF's mutations to the genome
sample = grumpy.mutate(ref, vcf)

# Get the genome level differences
genome_diff = grumpy.GenomeDifference(ref, sample)
for variant in genome_diff.variants:
    print(variant.variant)
# And minor alleles
for variant in genome_diff.minor_variants:
    print(variant.variant)

# Get gene level differences for all genes with mutations
for gene_name in sample.genes_with_mutations:
    print(gene_name)
    gene_diff = grumpy.GeneDifference(
            ref.get_gene(gene_name),
            sample.get_gene(gene_name),
            grumpy.MinorType.COV,
        )
    for mutation in gene_diff.mutations:
        print(mutation.mutation)
    # And minor alleles
    for mutation in gene_diff.minor_mutations:
        print(mutation.mutation)

线程

默认情况下，VCF解析将以与CPU核心数量相同的线程数运行。这可以为复杂的VCF文件带来显著的速度提升

要强制单线程（或指定线程数），运行 grumpy.thread_setup(<thread count>)。注意，应在调用此库中的任何其他函数之前运行，并且只能调用一次！不遵守此规则将导致错误！

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版本历史 发布通知 | RSS源

本版本

0.2.1

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bio_grumpy-0.2.1-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl (736.0 kB 查看哈希值)

上传于 CPython 3.8 manylinux: glibc 2.12+ i686

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