GenomeUtils

User Guide

  • Getting started
    • Installation
    • Core concepts
    • Complete workflow example
    • Building from existing files
    • Minimal in-memory example
    • Next steps

API Reference

  • API reference
    • GenomeUtils.Downloaders
      • Downloader
        • Downloader.cleanup()
        • Downloader.download_file()
      • EnsemblGenomeDownloader
        • EnsemblGenomeDownloader.download()
    • GenomeUtils.Genome
      • Chromosome
        • Chromosome.add_gene()
        • Chromosome.genes
        • Chromosome.get_subsequence_by_locus()
        • Chromosome.sequence
      • Exon
        • Exon.add_to_transcript()
        • Exon.get_gene()
        • Exon.get_transcripts()
        • Exon.sequence
      • Gene
        • Gene.add_transcript()
        • Gene.get_chromosome()
        • Gene.sequence
        • Gene.transcripts
      • Genome
        • Genome.add_chromosome()
        • Genome.chromosome_by_id()
        • Genome.chromosomes
        • Genome.exon_by_id()
        • Genome.exons
        • Genome.gene_by_id()
        • Genome.genes
        • Genome.get_sequence_by_locus()
        • Genome.index()
        • Genome.transcript_by_id()
        • Genome.transcripts
      • GenomeBuilder
        • GenomeBuilder.build()
        • GenomeBuilder.set_chromosome_filter()
        • GenomeBuilder.with_cdna_fasta()
        • GenomeBuilder.with_dna_fasta()
        • GenomeBuilder.with_gtf_file()
      • GenomeElement
        • GenomeElement.chr
        • GenomeElement.end
        • GenomeElement.parent
        • GenomeElement.sequence
        • GenomeElement.start
        • GenomeElement.strand
      • Locus
        • Locus.chr
        • Locus.contains()
        • Locus.end
        • Locus.overlaps()
        • Locus.start
        • Locus.strand
      • Transcript
        • Transcript.add_exon()
        • Transcript.exon_intervals()
        • Transcript.exons
        • Transcript.get_gene()
        • Transcript.sequence
        • Transcript.transcript_to_genomic_pos()

Project Info

  • License
  • Contributors
GenomeUtils
  • Search

© Copyright 2025, Alexander Schliep. Last updated on 2025-10-14.

Built with Sphinx using a theme provided by Read the Docs.