Masker.py - Wrapper for sequence masking tools¶
- Tags
Python
Code¶
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class
Masker.
Masker
¶ Bases:
object
a masker preserves gaps, but it does not preserve whitespace characters.
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getAlphabet
(sequence)¶ get sequence type (aa,na,codons).
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maskSequence
(peptide_sequence)¶ mask peptide sequence
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maskSequences
(sequences)¶ mask a collection of sequences.
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-
class
Masker.
MaskerBias
¶ Bases:
Masker.Masker
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class
Masker.
MaskerSeg
¶ Bases:
Masker.Masker
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class
Masker.
MaskerDustMasker
¶ Bases:
Masker.Masker
use dustmasker. masked chars are returned as lower case characters.
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class
Masker.
MaskerRandom
(proportion=10, *args, **kwargs)¶ Bases:
Masker.Masker
randomly mask a proportion of positions in a sequence in multiple alignment.
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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