tools.tileGenome

Help Info

Little tool to generate regions that tile the genome, excluding a set of regions that you specify.

usage: tileGenome [-h] [--genome GENOME]
                  [--allow-chrom ALLOWCHROM]
                  [--all-chroms]
                  [--output-length OUTPUTLENGTH]
                  [--input-length INPUTLENGTH]
                  [--chrom-edge-boundary CHROMEDGEBOUNDARY]
                  [--spacing SPACING]
                  [--output-bed OUTPUTBED]
                  [--blacklist BLACKLIST] [--verbose]

Named Arguments

--genome

The fasta-format genome file to tile.

--allow-chrom

A chromosome to allow in your tiled set. May be given multiple times.

--all-chroms

Instead of listing the chromosomes to use, use all of the chromosomes in the genome. Cannot be used with –allow-chrom.

Default: False

--output-length

The width of the output regions.

--input-length

The width of the model input.

--chrom-edge-boundary

How far from the chromosome edges should the tiled regions start?

--spacing

The space between regions.

--output-bed

The bed file that will be written.

--blacklist

A bed file of regions to exclude. May be given multiple times.

--verbose

Display progress messages

Default: False

Usage

A simple tool to generate a bed file that tiles a genome.

bpreveal.tools.tileGenome.getParser()

Generate the parser.

bpreveal.tools.tileGenome.main()

Actually run the tiling step.