`gumpy` re-implementation in Rust

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Project description

grumpy - Re-implementation of gumpy in Rust for speed

Does not implement the same interface, but rather the same premise.

Up to 100x faster than gumpy

Install

pip install bio-grumpy

Usage

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(
            reference.get_gene(gene_name),
            sample.get_gene(gene_name),
            get_minority_population_type(resistanceCatalogue),
        )
    for mutation in gene_diff.mutations:
        print(mutation.mutation)
    # And minor alleles
    for mutation in gene_diff.minor_mutations:
        print(mutation.mutation)

Project details

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Release history Release notifications | RSS feed

0.2.2

Oct 9, 2024

0.2.1

Oct 3, 2024

0.2.0

Aug 27, 2024

0.1.14

Aug 20, 2024

0.1.13

Aug 20, 2024

0.1.12

Aug 19, 2024

0.1.11

Aug 16, 2024

0.1.10

Jul 25, 2024

0.1.9

Jul 24, 2024

0.1.8

Jul 23, 2024

0.1.7

Jul 23, 2024

0.1.6

Jul 22, 2024

0.1.5

Jul 22, 2024

0.1.4

Jul 22, 2024

0.1.3

Jul 22, 2024

0.1.2

Jul 22, 2024

This version

0.1.1

Jul 19, 2024

0.1.0

Jul 19, 2024

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grumpy - Re-implementation of gumpy in Rust for speed

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