python/cython wrapper for fastahack library The c++ library, fastahack, reads .fai files files for an index, as created by e.g. samtools and the fastahack commandline interface. Currently, the index (chr => (position, line length)) is read into memory.
>>> from fastahack import FastaHack >>> f = FastaHack('fastahack/tests/correct.fasta') >>> f['1:1-10'] 'TAACCCTAAC' >>> f.get_sub_sequence('1', 0, 10) 'TAACCCTAACC' >>> f.get_sequence('1')[1:11] 'AACCCTAACC' >>> f.get_sequence_length('1') 630L >>> f.names ['1', '2', '3']
If python setup.py install gives an error, you may need to run cython fastahack/cfastahack.pyx