Pyllelic

Contents:

  • Welcome to Pyllelic’s documentation!
    • Quickstart
    • Demo gif
  • Dependencies and Installation
    • Using Conda (preferred)
    • Docker container
    • PyPi installation
  • Quickstart
    • Example exploratory use in jupyter notebook
  • Function Reference
    • pyllelic package
      • Submodules
      • pyllelic.config module
        • Config
      • pyllelic.process module
        • FileNameError
        • ShellCommandError
        • bismark()
        • bowtie2_fastq_to_bam()
        • build_bowtie2_index()
        • convert_methbank_bed()
        • fastq_to_list()
        • index_bam()
        • make_records_to_dictionary()
        • prepare_genome()
        • retrieve_seq()
        • sort_bam()
      • pyllelic.pyllelic module
        • AD_stats
        • BamOutput
        • GenomicPositionData
        • QumaResult
        • configure()
        • make_list_of_bam_files()
        • pyllelic()
      • pyllelic.quma module
        • Fasta
        • Quma
        • Reference
        • Result
      • pyllelic.visualization module
        • _create_heatmap()
        • _create_histogram()
        • _create_methylation_diffs_bar_graph()
        • _make_binary()
        • _make_methyl_df()
        • _make_stacked_fig()
        • _make_stacked_mpl_fig()
        • _make_stacked_plotly_fig()
      • pyllelic.main module
        • run_pyllelic()
  • Authors
  • pyllelic package
    • Submodules
    • pyllelic.config module
      • Config
        • Config.analysis_directory
        • Config.base_directory
        • Config.chromosome
        • Config.fname_pattern
        • Config.offset
        • Config.promoter_end
        • Config.promoter_file
        • Config.promoter_start
        • Config.results_directory
        • Config.viz_backend
    • pyllelic.process module
      • FileNameError
      • ShellCommandError
      • bismark()
      • bowtie2_fastq_to_bam()
      • build_bowtie2_index()
      • convert_methbank_bed()
      • fastq_to_list()
      • index_bam()
      • make_records_to_dictionary()
      • prepare_genome()
      • retrieve_seq()
      • sort_bam()
    • pyllelic.pyllelic module
      • AD_stats
        • AD_stats.crits
        • AD_stats.sig
        • AD_stats.stat
      • BamOutput
        • BamOutput.genome_values
        • BamOutput.name
        • BamOutput.positions
        • BamOutput.values
      • GenomicPositionData
        • GenomicPositionData.allelic_data
        • GenomicPositionData.cell_types
        • GenomicPositionData.config
        • GenomicPositionData.diffs
        • GenomicPositionData.file_names
        • GenomicPositionData.files_set
        • GenomicPositionData.from_pickle()
        • GenomicPositionData.generate_ad_stats()
        • GenomicPositionData.heatmap()
        • GenomicPositionData.histogram()
        • GenomicPositionData.individual_data
        • GenomicPositionData.means
        • GenomicPositionData.modes
        • GenomicPositionData.positions
        • GenomicPositionData.quma_results
        • GenomicPositionData.reads_graph()
        • GenomicPositionData.save()
        • GenomicPositionData.save_pickle()
        • GenomicPositionData.sig_methylation_differences()
        • GenomicPositionData.summarize_allelic_data()
        • GenomicPositionData.write_means_modes_diffs()
      • QumaResult
        • QumaResult.quma_output
        • QumaResult.values
      • configure()
      • make_list_of_bam_files()
      • pyllelic()
    • pyllelic.quma module
      • Fasta
        • Fasta.com
        • Fasta.pos
        • Fasta.seq
      • Quma
        • Quma.data
        • Quma.values
      • Reference
        • Reference.dir
        • Reference.exc
        • Reference.fasta
        • Reference.gdir
        • Reference.res
      • Result
        • Result.aliLen
        • Result.aliMis
        • Result.conv
        • Result.gAli
        • Result.gap
        • Result.match
        • Result.menum
        • Result.pconv
        • Result.perc
        • Result.qAli
        • Result.unconv
        • Result.val
    • pyllelic.visualization module
      • _create_heatmap()
      • _create_histogram()
      • _create_methylation_diffs_bar_graph()
      • _make_binary()
      • _make_methyl_df()
      • _make_stacked_fig()
      • _make_stacked_mpl_fig()
      • _make_stacked_plotly_fig()
    • pyllelic.main module
      • run_pyllelic()
Pyllelic
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© Copyright 2021, Andrew J. Bonham.

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