ALLCools.motif.motifs

Module Contents

_get_motif_threshold(motif, method, threshold_value)[source]
_single_seq_single_motif_max_score(seq, motif, threshold)[source]
class MotifSet(motifs, meta_table=None, motif_cluster_col='cluster_id')[source]
calculate_threshold(self, method='balanced', cpu=1, threshold_value=1000)[source]
_multi_seq_motif_scores(self, seq_list, save_path, region_dim, motif_dim, dtype)[source]
_run_motif_scan_chunks(self, fasta_path, output_dir, region_dim, motif_dim, dtype, chunk_size=10000, cpu=1)[source]
_aggregate_motif_clusters(self, output_dir, motif_dim, region_dim, dtype, chunk_size=1000000)[source]
scan_motifs(self, fasta_path, output_dir, cpu, region_dim, motif_dim='motif', combine_cluster=True, dtype='uint16', chunk_size=10000)[source]
class Motif(alphabet='ACGT', instances=None, counts=None)[source]

Bases: Bio.motifs.Motif

A class representing sequence motifs.