def get_fasta(self, id_): """Returns FASTA string given a valid identifier .. seealso:: :mod:`bioservices.apps.fasta` for dedicated tools to manipulate FASTA """ from bioservices.apps.fasta import FASTA f = FASTA() f.load_fasta(id_) return f.fasta
def get_fasta_sequence(self, id_): """Returns FASTA sequence (Not FASTA) :param str id_: Should be the entry name :return: returns fasta sequence (string) .. warning:: this is the sequence found in a fasta file, not the fasta content itself. The difference is that the header is removed and the formatting of end of lines every 60 characters is removed. """ from bioservices.apps.fasta import FASTA f = FASTA() f.load_fasta(id_) return f.sequence
def test_fasta(): fasta = FASTA() fasta.load_fasta(None) fasta.load_fasta("P43403") fasta.load_fasta("P43403") # already there fasta.header fasta.gene_name fasta.sequence fasta.fasta fasta.identifier fh = tempfile.NamedTemporaryFile(delete=False) fasta.save_fasta(fh.name) fasta.read_fasta(fh.name) fh.delete = True fh.close()