Installation
Bioconda
mamba install -c conda-forge -c bioconda wasp2
PyPI
pip install wasp2
The PyPI package does not install external tools such as samtools,
bcftools, or bedtools; install those separately.
Docker
docker pull ghcr.io/mcvickerlab/wasp2:1.4.1
docker run --rm ghcr.io/mcvickerlab/wasp2:1.4.1 wasp2-count --help
Singularity/Apptainer
singularity pull wasp2.sif docker://ghcr.io/mcvickerlab/wasp2:1.4.1
singularity exec wasp2.sif wasp2-count --help
CLI Tools
WASP2 installs three command-line entry points:
wasp2-mapwasp2-countwasp2-analyze
Quick Start
1. Correct mapping bias
wasp2-map make-reads input.bam variants.vcf.gz -s sample1 -o remap_dir
# Realign remap_dir/*_swapped_alleles_r1.fq and r2.fq with the same aligner
# and settings used for the original BAM, then:
wasp2-map filter-remapped remapped.bam \
-j remap_dir/input_wasp_data_files.json \
-o filtered.bam
2. Count alleles
wasp2-count count-variants filtered.bam variants.vcf.gz -s sample1 -o counts.tsv
3. Test for imbalance
wasp2-analyze find-imbalance counts.tsv -o ai_results.tsv
Single-Cell Example
wasp2-count count-variants-sc \
cellranger.bam \
variants.vcf.gz \
barcodes.tsv \
--samples sample1 \
--feature genes.gtf \
--out_file allele_counts.h5ad
wasp2-analyze find-imbalance-sc \
allele_counts.h5ad \
barcode_groups.tsv \
--sample sample1 \
-o ai_results.tsv
See the documentation for complete usage, tutorials, and API details.
1 maintainer
Metadata
1 maintainer
Release files for wasp2 1.4.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| wasp2-1.4.1.tar.gz | 174.6 kB | Without provenance | Details for wasp2-1.4.1.tar.gz |
Built distributions (wheels)
Total release size: 142.8 MB
Release files / wasp2-1.4.1.tar.gz
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Release files / wasp2-1.4.1-cp313-cp313-manylinux_2_28_x86_64.whl
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Release files / wasp2-1.4.1-cp313-cp313-manylinux_2_28_aarch64.whl
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Release files / wasp2-1.4.1-cp313-cp313-macosx_13_0_x86_64.whl
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Release files / wasp2-1.4.1-cp313-cp313-macosx_11_0_arm64.whl
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Release files / wasp2-1.4.1-cp312-cp312-manylinux_2_28_x86_64.whl
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Release files / wasp2-1.4.1-cp312-cp312-manylinux_2_28_aarch64.whl
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Release files / wasp2-1.4.1-cp312-cp312-macosx_13_0_x86_64.whl
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Release files / wasp2-1.4.1-cp311-cp311-manylinux_2_28_aarch64.whl
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Release files / wasp2-1.4.1-cp311-cp311-macosx_13_0_x86_64.whl
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Release files / wasp2-1.4.1-cp311-cp311-macosx_11_0_arm64.whl
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Release files / wasp2-1.4.1-cp310-cp310-manylinux_2_28_x86_64.whl
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Security for wasp2 1.4.1
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