def test_get_representatives(self):
"""get_representatives should return the representatives as list of Sequence."""
result = """>1: 5
ABABABA
>3: 1
BABA
>4: 1
ABABAA
>8: 2
BABBA
"""
seqs = self.data.iteritems
mapping = self.mapping
test_result = list(get_representatives(mapping, seqs()))
test_result_as_fasta = "".join(map(lambda a: a.to_fasta(),
test_result))
self.assertEqual(test_result_as_fasta, result)
# another example
mapping = {'1': ('a', 'b', 'c'), '2': ('d', 'e', 'f')}
seqs = [('1', "ACGT"), ('2', "TAGC"), ('a', "TTTTT")]
observed = list(get_representatives(mapping, seqs))
expected = [
BiologicalSequence("ACGT", id="1"),
BiologicalSequence("TAGC", id='2')
]
self.assertEqual(observed, expected)
def test_get_representatives(self):
"""get_representatives should return the representatives as list of Sequence."""
result= """>1: 5
ABABABA
>3: 1
BABA
>4: 1
ABABAA
>8: 2
BABBA"""
seqs = self.data.iteritems
mapping = self.mapping
test_result = list(get_representatives(mapping, seqs()))
test_result_as_fasta = "\n".join(map(lambda a: a.toFasta(),test_result))
self.assertEqual(test_result_as_fasta, result)
#another example
mapping = {'1': ('a','b','c'),
'2': ('d','e','f')}
seqs = [('1',"ACGT"), ('2', "TAGC"), ('a',"TTTTT")]
observed = list(get_representatives(mapping, seqs))
expected = [Sequence(name = ">1", seq="ACGT"), Sequence(name='2',
seq="TAGC")]
self.assertEqual(observed, expected)
def print_rep_seqs(mapping, seqs, out_fp):
"""Print the cluster seeds of a mapping to out_fp.
mapping: a cluster mapping
seqs: a list of seqs contained in the mapping
out_fp: output directory
"""
out_fh = open(out_fp + "/prefix_dereplicated.fasta", "w")
for s in (get_representatives(mapping, seqs.iteritems())):
out_fh.write(s.toFasta() + "\n")
out_fh.close()
def print_rep_seqs(mapping, seqs, out_fp):
"""Print the cluster seeds of a mapping to out_fp.
mapping: a cluster mapping
seqs: a list of seqs contained in the mapping
out_fp: output directory
"""
out_fh = open(out_fp + "/prefix_dereplicated.fasta", "w")
for s in (get_representatives(mapping, seqs.iteritems())):
out_fh.write(s.to_fasta())
out_fh.close()