def test_dereplicate_seqs_remove_singletons(self):
""" Test dereplicate_seqs() method functionality with
removing singletons
"""
seqs = [("seq1", "TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG"),
("seq2", "TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG"),
("seq3", "TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG"),
("seq4", "TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCT"),
("seq5", "TACCAGCCCCTTAAGTGGTAGGGACGATTATTTGGCCTAAAGCGTCCG"),
("seq6", "CTGCAAGGCTAGGGGGCGGGAGAGGCGGGTGGTACTTGAGGGGAGAAT"),
("seq7", "CTGCAAGGCTAGGGGGCGGGAGAGGCGGGTGGTACTTGAGGGGAGAAT")]
seqs_fp = join(self.working_dir, "seqs.fasta")
with open(seqs_fp, 'w') as seqs_f:
for seq in seqs:
seqs_f.write(">%s\n%s\n" % seq)
output_fp = join(self.working_dir, "seqs_derep.fasta")
log_fp = join(self.working_dir, "seqs_derep.log")
dereplicate_seqs(seqs_fp=seqs_fp, output_fp=output_fp)
self.assertTrue(isfile(output_fp))
self.assertTrue(isfile(log_fp))
exp = [("seq1;size=3;",
"TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG"),
("seq6;size=2;",
"CTGCAAGGCTAGGGGGCGGGAGAGGCGGGTGGTACTTGAGGGGAGAAT")]
with open(output_fp, 'U') as out_f:
act = [item for item in parse_fasta(out_f)]
self.assertEqual(act, exp)
def test_dereplicate_seqs(self):
""" Test dereplicate_seqs() method functionality,
keep singletons
"""
seqs = [("seq1", "TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG"),
("seq2", "TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG"),
("seq3", "TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG"),
("seq4", "TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCT"),
("seq5", "TACCAGCCCCTTAAGTGGTAGGGACGATTATTTGGCCTAAAGCGTCCG"),
("seq6", "CTGCAAGGCTAGGGGGCGGGAGAGGCGGGTGGTACTTGAGGGGAGAAT"),
("seq7", "CTGCAAGGCTAGGGGGCGGGAGAGGCGGGTGGTACTTGAGGGGAGAAT")]
seqs_fp = join(self.working_dir, "seqs.fasta")
with open(seqs_fp, 'w') as seqs_f:
for seq in seqs:
seqs_f.write(">%s\n%s\n" % seq)
output_fp = join(self.working_dir, "seqs_derep.fasta")
dereplicate_seqs(seqs_fp=seqs_fp, output_fp=output_fp, min_size=1)
self.assertTrue(isfile(output_fp))
exp = [("seq1;size=3",
"TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG"),
("seq6;size=2",
"CTGCAAGGCTAGGGGGCGGGAGAGGCGGGTGGTACTTGAGGGGAGAAT"),
("seq4;size=1",
"TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCT"),
("seq5;size=1",
"TACCAGCCCCTTAAGTGGTAGGGACGATTATTTGGCCTAAAGCGTCCG")]
act = [item for item in sequence_generator(output_fp)]
self.assertEqual(act, exp)
def test_dereplicate_seqs_remove_singletons(self):
""" Test dereplicate_seqs() method functionality with
removing singletons
"""
seqs = [("seq1", "TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG"),
("seq2", "TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG"),
("seq3", "TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG"),
("seq4", "TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCT"),
("seq5", "TACCAGCCCCTTAAGTGGTAGGGACGATTATTTGGCCTAAAGCGTCCG"),
("seq6", "CTGCAAGGCTAGGGGGCGGGAGAGGCGGGTGGTACTTGAGGGGAGAAT"),
("seq7", "CTGCAAGGCTAGGGGGCGGGAGAGGCGGGTGGTACTTGAGGGGAGAAT")]
seqs_fp = join(self.working_dir, "seqs.fasta")
with open(seqs_fp, 'w') as seqs_f:
for seq in seqs:
seqs_f.write(">%s\n%s\n" % seq)
output_fp = join(self.working_dir, "seqs_derep.fasta")
log_fp = join(self.working_dir, "seqs_derep.log")
dereplicate_seqs(seqs_fp=seqs_fp,
output_fp=output_fp)
self.assertTrue(isfile(output_fp))
self.assertTrue(isfile(log_fp))
exp = [("seq1;size=3;",
"TACCGGCAGCTCAAGTGATGACCGCTATTATTGGGCCTAAAGCGTCCG"),
("seq6;size=2;",
"CTGCAAGGCTAGGGGGCGGGAGAGGCGGGTGGTACTTGAGGGGAGAAT")]
with open(output_fp, 'U') as out_f:
act = [item for item in parse_fasta(out_f)]
self.assertEqual(act, exp)