ALLCools.sandbox.motif.ame
Contents
ALLCools.sandbox.motif.ame¶
Module Contents¶
- ame(bed_file, motif_files, output_path, reference_fasta, background_files=None, cpu=1, standard_length=None, chrom_size_path=None, ame_kws=None, sample=None, seed=1)[source]¶
Motif enrichment analysis with AME from MEME Suite.
- Parameters
bed_file – Single bed file input to calculate motif enrichment
motif_files – One or multiple motif files in MEME format
output_path – Output path of the AME result
reference_fasta – Reference fasta of the bed_file and background_files
background_files – One or multiple bed files contain region as the control set of motif enrichment
cpu – Number of CPUs to parallel AME
standard_length – If not None, will standard the input region and control region (if provided) in to same standard_length, each standardized region is centered to the original region center.
chrom_size_path – {chrom_size_path_doc} Must provide is standard_length is not None.
ame_kws – Additional options that will pass to AME, provide either a dict or string. If string provided, will directly insert into the final AME command, see AME documentation about AME options. e.g. ‘–seed 1 –method fisher –scoring avg’
sample – Sample input regions to this number to reduce run time or test
seed – Seed for random sample input regions, only apply when sample is not None