DNA Module API Documentation

DNA Module API Documentation#

The DNA module provides functionality for working with DNA sequences, motifs, mutations, and genomic regions.

Classes#

DNASequence#

  • Description: Base class for representing and manipulating DNA sequences. Inherits from Seq in Biopython.

  • Key Methods:

    • get_reverse_complement(): Returns the reverse complement sequence.

    • padding(left=0, right=0, target_length=0): Pads sequence with N’s.

    • mutate(pos, alt): Creates new sequence with mutation at specified position.

    • one_hot: Property that returns one-hot encoded sequence.

DNASequenceCollection#

  • Description: Collection of DNASequence objects with methods for batch operations.

  • Key Methods:

    • from_fasta(filename): Creates collection from FASTA file.

    • mutate(pos_list, alt_list): Applies mutations to sequences.

    • scan_motif(motifs): Scans sequences for motif matches.

    • save_zarr(): Saves sequences in Zarr format.

Motif Analysis#

Motif

Base class for TFBS motifs.

MotifCluster

Base class for TFBS motif clusters.

Motif#

  • Description: Base class for transcription factor binding site motifs.

  • Key Methods:

    • plot_logo(): Plots sequence logo for motif.

    • __repr__(): String representation of motif.

MotifCluster#

  • Description: Collection of related motifs.

  • Key Methods:

    • get_gene_name_list(): Gets associated gene names.

Track Visualization#

Track

A class to represent and manipulate genomic track data.

Track#

  • Description: Class for visualizing genomic tracks.

  • Key Methods:

    • plot_tracks(): Plots tracks with optional gene annotations.

    • plot_tracks_with_motif_density(): Plots tracks with motif density.

    • generate_bedgraph(): Exports track as bedGraph.

    • generate_bigwig(): Exports track as BigWig.