def test_schema_representation(self):
"""Convert sequences into schema representations.
"""
# get a set of schemas we want to code the sequence in
schema_bank = self._load_schema_repository()
top_schemas = schema_bank.get_top(25)
schema_coder = Schema.SchemaCoder(top_schemas, self.schema)
# get the sequences one at a time, and encode them
fasta_handle = open(self.test_file, 'r')
seq_parser = Fasta.SequenceParser(alphabet=IUPAC.unambiguous_dna)
iterator = Fasta.Iterator(fasta_handle, seq_parser)
while 1:
seq_record = iterator.next()
if seq_record is None:
break
schema_values = schema_coder.representation(seq_record.seq)
if VERBOSE:
print "Schema values:", schema_values
fasta_handle.close()
def test_schema_representation(self):
"""Convert sequences into schema representations."""
# get a set of schemas we want to code the sequence in
schema_bank = self._load_schema_repository()
top_schemas = schema_bank.get_top(25)
schema_coder = Schema.SchemaCoder(top_schemas, self.schema)
# get the sequences one at a time, and encode them
fasta_handle = open(self.test_file, 'r')
for seq_record in SeqIO.parse(fasta_handle, "fasta",
alphabet=IUPAC.unambiguous_dna):
schema_values = schema_coder.representation(seq_record.seq)
if VERBOSE:
print("Schema values: %s" % schema_values)
fasta_handle.close()
def setUp(self):
ambiguity_chars = {"G" : "G",
"A" : "A",
"T" : "T",
"C" : "C",
"R" : "AG",
"*" : "AGTC"}
motif_representation = Schema.Schema(ambiguity_chars)
motifs = ("GA", "GATAG", "GA*AG", "GATRG", "*A")
self.motif_coder = Schema.SchemaCoder(motifs,
motif_representation)
self.match_strings = [("GATAG", [.5, .5, .5, .5, 1.0]),
("GAGAGATA", [float(3) / float(4), 0,
float(1) / float(4), 0,
1])]
