Contents

ALLCools.sandbox.motif.fimo

ALLCools.sandbox.motif.fimo

Run FIMO to scan motif over FASTA sequences

Module Contents

_fimo_runner(motif_path, fasta_path, output_path, path_to_fimo='', raw_score_thresh=6, raw_p_value_thresh=0.0005, is_genome_fasta=False, top_n=300000)[source]

Run fimo for a single motif over single fasta file

_scan_motif_over_fasta(meme_motif_file, fasta_path, cpu, output_dir, path_to_fimo='', raw_score_thresh=7, raw_p_value_thresh=0.0005, top_n=300000, is_genome_fasta=False)[source]
_aggregate_motif_beds(bed_file_paths, output_path, cpu=1, sort_mem_gbs=1)[source]

previous

ALLCools.sandbox.motif.cmotif

next

ALLCools.sandbox.motif.motif_scan