def test_load_fasta_align():
"""
This tests load_fasta_align using toy_data's fastas.
"""
aminobet = "-ACDEFGHIKLMNPQRSTVWY"
def ring_pop(amino_str):
out = amino_str[-1]
amino_str = amino_str[:-1]
return out + amino_str
seq_loc = join(dirname(__file__),pardir)
mod_loc = join(seq_loc,pardir)
toy_loc = join(mod_loc,"toy_data")
fas_loc = join(toy_loc,"toy_fastas")
#test cycled
cyc_loc = join(fas_loc,toy_fastas["cyc"])
cyc_aln = load_fasta_align(cyc_loc)
assert len(cyc_aln) == 210
assert sum([int(seq_id) for seq_id in cyc_aln]) == \
sum(xrange(210))
for i in xrange(210):
assert cyc_aln[str(i)] == aminobet
aminobet = ring_pop(aminobet)
def load_toy_data(subset="two_seq"):
""" Valid subsets are:
cyc_seq : A 21x210 fasta of all of the standard
aminoalphabet and a gap.
two_seq : The first two sequences from cyc_seq.
pmm_seq : A MUSCLE alignment of phosphomannomutase
retrieved from the PIR on Apr 3, 2012.
"""
file_handle = data_names[subset]
if subset[-3:] == 'seq':
return load_fasta_align(file_handle)
