Package genome

modules for dealing with (mainly importing to datasets) genomic data

Submodules

dimer.genome.bed: Iterator for the BED format ( http://genome.ucsc.edu/FAQ/FAQformat.html#format1 ) Returns chrom, chromStart, chromEnd, name, score
dimer.genome.bedops: wrapper to some of the bedops (http://code.google.com/p/bedops/) utilities
dimer.genome.bedops_tests
dimer.genome.peak: Iterator for the broadPeak and narrowPeak formats (http://genome.ucsc.edu/FAQ/FAQformat.html#format13 and https://genome.ucsc.edu/FAQ/FAQformat.html#format12)

Functions

parseBED(s, use_score=True, bg_val=1.0)
parse a feature in BED4 or BED5 format

source code

Variables

__package__ = None

Function Details

parse a feature in BED4 or BED5 format

s: tab-separated line from the BED file use_score: use the score of the feature or set it to bg_val return: BED5+ feature