def test_writeread(self):
f = tempfile.TemporaryFile('w+r')
matchfile.save(self.matches, f)
f.seek(0)
m2 = matchfile.load(f, self.hmms, self.targets)
check_valid(self, m2)
f.close()
def test_jackhmmer(self):
seq = SeqIO.read('tests/data/jackhmmer_seq.fasta', 'fasta',
alphabet=Alphabet.generic_protein)
seqdb = SeqIO.read('tests/data/matchtarget.fasta', 'fasta',
alphabet=Alphabet.generic_protein)
j = HMMER.jackhmmer(seq, seqdb)
#load the expected output
seq_ = HMMER.wrap_seqrecords([seq,])
seqdb_ = HMMER.wrap_seqrecords([seqdb,])
m = matchfile.load('tests/data/jack_out', seq_, seqdb_)
self.assertEqual(m, j.matches)
def test_jackhmmer_dna(self):
seq = SeqIO.read('tests/data/jackhmmer_seq.fasta', 'fasta',
alphabet=Alphabet.generic_protein)
seqdb = SeqIO.read('tests/data/dna_target.fasta', 'fasta',
alphabet=Alphabet.generic_dna)
j = HMMER.jackhmmer(seq, seqdb)
#load the expected output
seqdb_prot = SeqIO.read('tests/data/matchtarget.fasta', 'fasta',
alphabet=Alphabet.generic_protein)
seq_ = HMMER.wrap_seqrecords([seq,])
seqdb_ = HMMER.wrap_seqrecords([seqdb_prot,])
matches = matchfile.load('tests/data/jack_out', seq_, seqdb_)
#scale the matches' locations to match the protein search
for m in matches:
m.scale(3)
self.assertEqual([str(m) for m in matches], [str(m) for m in j.matches])