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(
            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)

Threads

By default, VCF parsing will run with the same number of threads as CPU cores. This can give significant speed improvements for complex VCF files

To force single threading (or other number of threads), run grumpy.thread_setup(<thread count>). Note that should be run before any other function in this library, and should not be called more than once! Not following this will cause errors!

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for jeremy.westhead from gravatar.com jeremy.westhead

Credits

Author: Jeremy Westhead

License

Other/Proprietary License

Requires

Python <3.13, >=3.8

Classifiers

Report project as malware

Release files for bio-grumpy 1.1.4

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for bio-grumpy 1.1.4
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Built distributions (wheels)

Table of built distributions (wheels) for bio-grumpy 1.1.4
File
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bio_grumpy-1.1.4-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl 779.0 kB CPython 3.10 CPython 3.10 Linux glibc 2.17+ ARMv7l Details
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bio_grumpy-1.1.4-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.whl 790.6 kB CPython 3.10 CPython 3.10 Linux glibc 2.12+ x86-32 Details
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bio_grumpy-1.1.4-cp39-cp39-musllinux_1_2_i686.whl 999.4 kB CPython 3.9 CPython 3.9 Linux musl 1.2+ x86-32 Details
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bio_grumpy-1.1.4-cp38-cp38-manylinux_2_17_armv7l.manylinux2014_armv7l.whl 780.9 kB CPython 3.8 CPython 3.8 Linux glibc 2.17+ ARMv7l Details
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bio_grumpy-1.1.4-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl 789.4 kB CPython 3.8 CPython 3.8 Linux glibc 2.12+ x86-32 Details

Total release size: 74.4 MB

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