Welcome to bx-python’s documentation!
The bx-python project 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; optimized 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
These tools have been used in a variety of published research, and are a fundamental part of the ongoing Galaxy and ESPERR projects.
Contents:
- Application Documentation
- bx package
- Subpackages
- Submodules
- bx.binned_array module
- bx.binned_array_tests module
- bx.bitset module
- bx.bitset_builders module
- bx.bitset_tests module
- bx.bitset_utils module
- bx.filter module
- bx.gene_reader module
- bx.interval_index_file module
- bx.interval_index_file_tests module
- bx.seqmapping module
- bx.seqmapping_tests module
- bx.wiggle module
- bx.wiggle_tests module
- Module contents
- bx_extras package
- psyco_full module
- bx package