def sequences(self):
"""Generates each sequence in the genome as a FASTASequence
>>> from tigerlily.sequences import PolymerSequence
>>> refgen = GRCGenome.download('test1')
>>> for seq in refgen.sequences():
... isinstance(seq,PolymerSequence)
True
True
True
"""
if self._archive is None:
raise ValueError('Empty reference genome, no archive loaded')
for fasta_file in self._archive.getfasta():
for seq in parseFASTA(file=fasta_file):
yield seq
def _handle_arch(self,arch):
"handler for testing an Archive object regardless of format"
self.assertEqual(len(arch.getnames()),4)
fasta_files = [f for f in arch.getfasta()]
self.assertEqual(len(fasta_files),3)
nofasta_files = [f for f in arch.getnofasta()]
self.assertEqual(len(nofasta_files),1)
# Finally, just test to make sure that FASTA can handle the test files
# This isn't really a test of this unit, but it's a logical extension
# and it would be bad if it failed, so let's do the test.
for fasta_fileobj in arch.getfasta():
for fasta_seq in parseFASTA(fasta_fileobj):
self.assertTrue(len(fasta_seq.sequence) > 0)
self.assertTrue(fasta_seq.identifier.startswith('seq'))