genomepy.genome.sequences.track2fasta

genomepy.genome.sequences.track2fasta(self, track, fastafile=None, stranded=False, extend_up=0, extend_down=0)

Return a list of fasta sequences as Sequence objects as directed from the track(s).

Parameters

• track (list/region file/bed file) – region(s) you wish to translate to fasta. Example input files can be found in genomepy/tests/data/regions.*

• fastafile (bool , optional) – return Sequences as list or save to file? (default: list)

• stranded (bool , optional) – return sequences for both strands? Required BED6 (or higher) as input (default: False)

• extend_up (int , optional) – extend the sequences up? (command is strand sensitive, default: 0)

• extend_down (int , optional) – extend the sequences down? (command is strand sensitive, default: 0)