Masker.py - Wrapper for sequence masking tools

Tags

Python

Code

class Masker.Masker

Bases: object

a masker preserves gaps, but it does not preserve whitespace characters.

getAlphabet(sequence)

get sequence type (aa,na,codons).

maskSequence(peptide_sequence)

mask peptide sequence

maskSequences(sequences)

mask a collection of sequences.

class Masker.MaskerBias

Bases: Masker.Masker

class Masker.MaskerSeg

Bases: Masker.Masker

class Masker.MaskerDustMasker

Bases: Masker.Masker

use dustmasker. masked chars are returned as lower case characters.

class Masker.MaskerRandom(proportion=10, *args, **kwargs)

Bases: Masker.Masker

randomly mask a proportion of positions in a sequence in multiple alignment.

Masker.maskSequences(sequences, masker=None)

return a list of masked sequence.

masker can be one of

dust/dustmasker * run dustmasker on sequences softmask * use softmask to hardmask sequences