Efficient "pythonic" access to FASTA files using pyfaidx [post]

Matthew D Shirley, Zhaorong Ma, Brent S Pedersen, Sarah J Wheelan
2015 PeerJ Preprints  
The pyfaidx Python module provides memory and time-efficient indexing, subsetting, and in-place modification of subsequences of FASTA files. pyfaidx provides Python classes that expose a dictionary interface where sequences from an indexed FASTA can be accessed by their header name and then sliced by position without reading the full file into memory. pyfaidx includes an extensive test suite to ensure correct and reproducible behavior. A command-line program (faidx) is also provided as an
more » ... rovided as an alternative interface, with significant enhancements to functionality, while maintaining full index file compatibility with samtools. The pyfaidx module is installable from PyPI (https://pypi.python.org/pypi/pyfaidx), and development versions can be found at Github (https://github.com/mdshw5/pyfaidx).
doi:10.7287/peerj.preprints.970v1 dblp:journals/peerjpre/ShirleyMPW15 fatcat:37aj65556vhbjmfas6taj6wd5u