MAST.py - Parser for MAST files

Author: Release:$Id$ Date:December 09, 2013 Tags:Python

As of biopython 1.5.6, the MAST parser is broken.

class MAST.Match

a MAST entry.

MAST.parse(infile)

parse verbose MAST output.

MAST.frequencies2logodds(counts, background_frequencies=None)

write a motif from counts to outfile.

Counts should be a numpy matrix with nalphabet columns and motif_width rows.

MAST.writeMast(outfile, logodds_matrix, alphabet)

output logodds matrix in MAST format.

MAST.writeTomTom(outfile, counts_matrix, header=False)

output counts matrix in tomtom format.

output counts with columns as motif positions and rows as alphabet.

MAST.sequences2motif(outfile, sequences, background_frequencies=None, format='MAST')

write a motif defined by a collection of sequences to outfile.