bx.align.sitemask package

Submodules

• bx.align.sitemask.core module
  • MaskPipeline
    • MaskPipeline.get_masked()
    • MaskPipeline.masked
  • Masker
• bx.align.sitemask.cpg module
  • Inclusive
  • Restricted
  • mask_columns()
  • nonCpG
• bx.align.sitemask.quality module
  • NQS
  • Simple
• bx.align.sitemask.sitemask_tests module
  • test_cpg_inclusive()
  • test_cpg_restricted()
  • test_non_cpg()

Module contents

Tools for masking out specific sites in aligments by various criteria, for example masking CpG sites or sites with low sequence quality.

class bx.align.sitemask.MaskPipeline(**kwargs)

Bases: Pipeline

MaskPipeline implements a Pipeline through which alignments can be pushed and masked. Pipelines can be aggregated.

get_masked()

property masked

class bx.align.sitemask.Masker(**kwargs)

Bases: Filter