bx.motif.io.transfac module

Classes for reading and writing motif data.

class bx.motif.io.transfac.TransfacMotif

Bases: object

class bx.motif.io.transfac.TransfacReader(input)

Bases: object

Reads motifs in TRANSFAC format.

as_dict(key='id')

Return a dictionary containing all remaining motifs, using key as the dictionary key.

next_motif()

parse_actions = {'AC': ('store_single', 'accession'), 'AT': ('store_single_key_value', 'attributes'), 'BA': ('store_block', 'basis'), 'BF': ('store_single_list', 'binding_factors'), 'BS': ('store_single_list', 'sites'), 'CC': ('store_block', 'comment'), 'DE': ('store_block', 'description'), 'DT': ('store_single_list', 'dates'), 'ID': ('store_single', 'id'), 'NA': ('store_single', 'name'), 'P0': ('store_matrix', 'matrix'), 'TY': ('store_single', 'type')}

parse_record(lines)

Parse a TRANSFAC record out of lines and return a motif.

class bx.motif.io.transfac.TransfacWriter(output)

Bases: object

Writes motifs in TRANSFAC format.

actions = {'AC': ('store_single', 'accession'), 'AT': ('store_single_key_value', 'attributes'), 'BA': ('store_block', 'basis'), 'BF': ('store_single_list', 'binding_factors'), 'BS': ('store_single_list', 'sites'), 'CC': ('store_block', 'comment'), 'DE': ('store_block', 'description'), 'DT': ('store_single_list', 'dates'), 'ID': ('store_single', 'id'), 'NA': ('store_single', 'name'), 'P0': ('store_matrix', 'matrix'), 'TY': ('store_single', 'type')}

write(motif)