Annotation Commands

Commands for mapping data to genomic features.

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match_region_annotation

Intersect identified regions (DMRs) with genomic annotations (e.g., GENCODE) to determine genomic context (promoters, exons, introns, etc.).

.. note:: Required columns in regions_df: ['chrom', 'chromStart', 'chromEnd']. If pipeline is enabled and regions_df is None, it defaults to the 'cluster_df' from the generate_DMR step.

Argument	Default	Description
--regions_df	None	Input dataframe containing genomic regions to annotate.
--ref_folder	None	Path to the reference genome folder.
--bed_file	CpG_gencode_annotation.bed	Filename of the annotation BED file located in the ref_folder, defaults to "CpG_gencode_annotation.bed"
--name	match_region_annotation	Prefix for output files, defaults to "match_region_annotation"
--annotation_or_region	region	Determines the perspective of the output overlap ("annotation" or "region"), defaults to "region"
--show_counts	False	If True, returns count statistics of the annotations, defaults to False

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match_position_annotation

Intersect single genomic positions (DMLs) with genomic annotations to determine local context.

.. note:: Required columns in regions_df: ['chrom', 'chromStart']. Similar to match_region_annotation, but optimized for single-base coordinate matching rather than range-based intersection.

Argument	Default	Description
--regions_df	None	Input dataframe containing genomic positions to annotate.
--ref_folder	None	Path to the reference genome folder.
--bed_file	CpG_gencode_annotation.bed	Filename of the annotation BED file, defaults to "CpG_gencode_annotation.bed"
--name	match_position_annotation	Prefix for output files, defaults to "match_position_annotation"

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map_positions_to_genes

Map positions to genes.

.. note:: Required columns for positions: - ["chromosome", "position_start", "diff"]

Argument	Default	Description
--positions	None	Position data. Not necessary if the pipeline is in use, defaults to None
--ref_folder	None	---
--gene_regions	['intron', 'exon', 'upstream', 'CCRE']	Gene regions to map to. Options are any combination of ["intron", "exon", "upstream", "CCRE"], defaults to ["intron", "exon", "upstream", "CCRE"]
--min_pos_diff	0	Minimum position difference for mapping, defaults to 0
--gtf_file	gencode.chr_patch_hapl_scaff.annotation.gtf	GTF annotation file with unflexible input format, defaults to "gencode.v42.chr_patch_hapl_scaff.annotation.gtf"
--bed_file	CpG_gencode_annotation.bed	BED annotation file with unflexible input format, defaults to "CpG_gencode_annotation.bed"
--pipeline_input_source	auto	Pipeline input source for pipelining, options are ["auto", "map_win_2_pos", "generate_q_values", "filters"], defaults to "auto"
--rerun	False	Rerun the analysis. If False, load previous output. Defaults to False.

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graph_upstream_UCSC

Generate a UCSC graph of upstream gene methylation.

.. note:: Required columns for position_data: - ["chromosome", "position_start", "methylation_percentage*"] - There must be a methylation_percentage column for each sample to plot.

Argument	Default	Description
--gene_name	*Required*	Gene name
--position_data	None	Position data
--ref_folder	None	---
--name	UCSC_graph.bedGraph	Output BEDGraph file name, defaults to "UCSC_graph.bedGraph"
--before_tss	5000	Distance before transcrption start site (TSS), defaults to 5000
--gtf_file	gencode.chr_patch_hapl_scaff.annotation.gtf	GTF file, defaults to "gencode.chr_patch_hapl_scaff.annotation.gtf"

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