darkprofiler 0.1.0

DarkProfiler: Alignment and Classification of Peptides from Reference-Independent De Novo Peptide Sequencing Experiments.

DarkProfiler

DarkProfiler: Alignment and Classification of Peptides from Reference-Independent De Novo Peptide Sequencing Experiments

DarkProfiler takes peptide sequences (e.g. from de novo sequencing) and classifies them into:

• Canonical proteome
• Alternative splicing
• Neoantigens (SNV-derived mutanome)
• Alternative reading frame peptides
• Amino acid misincorporations
• Unknown / unaligned

It supports human and mouse references: hg19, hg38, mm10, mm39.

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Installation

Install with pip (PyPI)

pip install darkprofiler

Install with conda (bioconda)

conda install bioconda::darkprofiler

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Reference genome

DarkProfiler supports human and mouse reference genomes.

Supported genome assemblies are:

hg19 (GENCODE release 19)
hg38 (GENCODE release 37)
mm10 (GENCODE release M19)
mm39 (GENCODE release M37)

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Command-line usage

Download reference data

darkprofiler download hg38

Run classification

darkprofiler run hg38 peptides.fa output_dir

Optional flags:

--vcf-path FILE
--database-path DIR
--num-threads N

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Python API

from darkprofiler.run import classify_peptides

classify_peptides(
    reference="hg38",
    peptide_fasta="peptides.fa",
    output_dir="output",
    vcf_path=None,
    database_path=None,
    num_threads=4
)

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Outputs

• canonicalProteome.fa
• alternativeSplicing.fa
• neoantigen.fa
• alternativeReadingFrame.fa
• aminoAcidMisincorporation.fa
• unknown.fa
• pieChart.tsv
• pieChart.pdf

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License

MIT License
Copyright (c) 2025