def test_truncate_rev_primers(self):
""" Properly truncates remove primers """
out_f = FakeOutFile()
rev_primers = {
'PC.481': ['CTCTCCG'],
'PC.634': ['CTCTCAG'],
'PC.635': ['CTCTCAG'],
'PC.636': ['CTCTCAG'],
'PC.354': ['CTCTCAG']
}
# Use default options, all sequences should get truncated and written
log_data = truncate_rev_primers(open(self.fasta_fp, "U"), out_f,
rev_primers)
expected_log_data = {
'seqs_written': 5,
'total_seqs': 6,
'sample_id_not_found': 0,
'reverse_primer_not_found': 0
}
self.assertEqual(log_data, expected_log_data)
# Note that because these are short sequences, two mismatches allows
# for a very short truncation of one of the sequences
self.assertEqual(out_f.data, self.expected_truncation_default_settings)
# With zero mismatches will not truncate all seqs
out_f = FakeOutFile()
# Use default options, all sequences should get truncated and written
log_data = truncate_rev_primers(open(self.fasta_fp, "U"),
out_f,
rev_primers,
primer_mismatches=0)
expected_log_data = {
'seqs_written': 5,
'total_seqs': 6,
'sample_id_not_found': 0,
'reverse_primer_not_found': 2
}
self.assertEqual(log_data, expected_log_data)
# With zero mismatches allowed, 2 seqs should not be truncated
self.assertEqual(out_f.data, self.expected_truncation_zero_mismatches)
# With zero mismatches and truncate_remove option, should only write
# 3 of the sequences
out_f = FakeOutFile()
log_data = truncate_rev_primers(open(self.fasta_fp, "U"),
out_f,
rev_primers,
truncate_option="truncate_remove",
primer_mismatches=0)
expected_log_data = {
'seqs_written': 3,
'total_seqs': 6,
'sample_id_not_found': 0,
'reverse_primer_not_found': 2
}
self.assertEqual(log_data, expected_log_data)
# With zero mismatches allowed, 3 seqs total should be written
self.assertEqual(
out_f.data,
self.expected_truncation_zero_mismatches_truncate_remove)
# Should count sample ids not found in log
out_f = FakeOutFile()
rev_primers = {
'PC.481': ['CTCTCCG'],
'PC.634': ['CTCTCAG'],
'PC.635': ['CTCTCAG'],
'PC.636': ['CTCTCAG'],
'PC.354': ['CTCTCAG']
}
# Use default options, all sequences should get truncated and written
log_data = truncate_rev_primers(open(self.fasta_badlabels_fp, "U"),
out_f, rev_primers)
expected_log_data = {
'seqs_written': 5,
'total_seqs': 5,
'sample_id_not_found': 5,
'reverse_primer_not_found': 0
}
self.assertEqual(log_data, expected_log_data)
# No matches to sample IDs, so sequences are written unmodified
self.assertEqual(out_f.data, self.sample_fasta_file_bad_labels_data)
def test_truncate_rev_primers(self):
""" Properly truncates remove primers """
out_f = FakeOutFile()
rev_primers = {'PC.481': ['CTCTCCG'], 'PC.634': ['CTCTCAG'],
'PC.635': ['CTCTCAG'], 'PC.636': ['CTCTCAG'], 'PC.354': ['CTCTCAG']}
# Use default options, all sequences should get truncated and written
log_data = truncate_rev_primers(open(self.fasta_fp, "U"),
out_f, rev_primers)
expected_log_data = {'seqs_written': 5, 'total_seqs': 6,
'sample_id_not_found': 0, 'reverse_primer_not_found': 0}
self.assertEqual(log_data, expected_log_data)
# Note that because these are short sequences, two mismatches allows
# for a very short truncation of one of the sequences
self.assertEqual(out_f.data, self.expected_truncation_default_settings)
# With zero mismatches will not truncate all seqs
out_f = FakeOutFile()
# Use default options, all sequences should get truncated and written
log_data = truncate_rev_primers(open(self.fasta_fp, "U"),
out_f, rev_primers, primer_mismatches=0)
expected_log_data = {'seqs_written': 5, 'total_seqs': 6,
'sample_id_not_found': 0, 'reverse_primer_not_found': 2}
self.assertEqual(log_data, expected_log_data)
# With zero mismatches allowed, 2 seqs should not be truncated
self.assertEqual(out_f.data, self.expected_truncation_zero_mismatches)
# With zero mismatches and truncate_remove option, should only write
# 3 of the sequences
out_f = FakeOutFile()
log_data = truncate_rev_primers(open(self.fasta_fp, "U"),
out_f, rev_primers, truncate_option="truncate_remove",
primer_mismatches=0)
expected_log_data = {'seqs_written': 3, 'total_seqs': 6,
'sample_id_not_found': 0, 'reverse_primer_not_found': 2}
self.assertEqual(log_data, expected_log_data)
# With zero mismatches allowed, 3 seqs total should be written
self.assertEqual(out_f.data,
self.expected_truncation_zero_mismatches_truncate_remove)
# Should count sample ids not found in log
out_f = FakeOutFile()
rev_primers = {'PC.481': ['CTCTCCG'], 'PC.634': ['CTCTCAG'],
'PC.635': ['CTCTCAG'], 'PC.636': ['CTCTCAG'], 'PC.354': ['CTCTCAG']}
# Use default options, all sequences should get truncated and written
log_data = truncate_rev_primers(open(self.fasta_badlabels_fp, "U"),
out_f, rev_primers)
expected_log_data = {'seqs_written': 5, 'total_seqs': 5,
'sample_id_not_found': 5, 'reverse_primer_not_found': 0}
self.assertEqual(log_data, expected_log_data)
# No matches to sample IDs, so sequences are written unmodified
self.assertEqual(out_f.data, self.sample_fasta_file_bad_labels_data)
