May 26, 2018

Python module for reading, manipulating and writing genomic data sets

bx-python is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are

Classes for reading and working with genome-scale multiple local alignments in MAF, AXT, and LAV formats. Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences used, for example, to provide random access to individual alignments in huge files; optomized for use over network filesystems. Data structures for working with intervals on sequences

  • “Binned bitsets” which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly
  • “Intersecter” for performing fast intersection tests that preserve both query and target intervals and associated annotation

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