gdata.GenomeDataBuilder#
- class gdata.GenomeDataBuilder(self, /, location, genome_fasta, window_size, *, segments=None, step_size=None, resolution=32, padding=0, chroms=None, temp_dir=None)#
Represents a builder for genomic data, allowing for the creation and management of genomic datasets.
This struct provides methods to create a new genomic dataset, open an existing dataset, and manage genomic data chunks. It supports operations like adding files, retrieving chromosome information, and iterating over data chunks.
- Parameters:
location – The directory where the genomic data will be stored.
genome_fasta – The path to the FASTA file containing the genome sequences.
window_size – The size of the genomic windows to be processed.
segments – Optional list of genomic segments to include in the dataset. The genomic segments should be provided as strings in the format “chrom:start-end”. If None, the entire genome will be used.
step_size – The step size for sliding the window across the genome (default is None, which uses
window_size).resolution – The resolution of the stored genomic data (default is 1).
padding – The amount of padding to add around each genomic segment (default is 0). Extra padding allows shifting the window within the padded region during data loading.
chroms – A list of chromosomes to include in the dataset. If None, all chromosomes in the FASTA file will be used.
temp_dir – Optional temporary directory for intermediate files. If None, a system temporary directory will be used.
See also
Examples
>>> from gdata import as GenomeDataBuilder >>> regions = ["chr11:35041782-35238390", "chr11:35200000-35300000"] >>> tracks = {'DNase:CD14-positive monocyte': 'ENCSR464ETX.w5z', 'DNase:keratinocyte': 'ENCSR000EPQ.w5z'} >>> builder = GenomeDataBuilder("genome.gdata", 'genome.fa.gz', segments=regions, window_size=196_608, resolution=128) >>> builder.add_files(tracks) >>> builder.finish()
Methods