Python trim_primer Examples

Example #1

File: strip_primer_tails_test.py Project: traeki/public-analyze-reads

 def testRNASeqTrimming(self):
   read = 'CATTCTGTGGAACGGTCCGGTTGGCGCTGTAGGCACCATCAATTCGTATG'
   self.primer_seq = SeqRecord(read)
   self.primer_seq.letter_annotations['phred_quality'] = [10] * len(read)
   primer = 'CTGTAGGCACCATCAAT'
   goal = 'CATTCTGTGGAACGGTCCGGTTGGCG'
   goal_seq = SeqRecord(goal)
   goal_seq.letter_annotations['phred_quality'] = [10] * len(goal)
   trimmed = strip.trim_primer(primer, self.primer_seq,
                               self.min_primer_match, self.max_primer_offset)
   self.assertTrue(same_sequence(trimmed, goal_seq),
       self.inequality_error.format(trimmed, self.baseline))

Example #2

File: strip_primer_tails_test.py Project: traeki/public-analyze-reads

 def testIgnoredOffsetPrimerTrimming(self):
   self.baseline = self.baseline[:-12] + self.primer_seq[4:16]
   trimmed = strip.trim_primer(self.primer, self.baseline,
                               self.min_primer_match, self.max_primer_offset)
   self.assertTrue(same_sequence(trimmed, self.baseline),
       self.inequality_error.format(trimmed, self.baseline))

Example #3

File: strip_primer_tails_test.py Project: traeki/public-analyze-reads

 def testTrivialTrimming(self):
   trimmed = strip.trim_primer(self.primer, self.baseline,
                               self.min_primer_match, self.max_primer_offset)
   self.assertTrue(same_sequence(trimmed, self.baseline),
       self.inequality_error.format(trimmed, self.baseline))

Example #4

File: strip_primer_tails_test.py Project: traeki/public-analyze-reads

 def testSimpleTrimming(self):
   self.baseline = self.baseline[:-len(self.primer)] + self.primer_seq
   trimmed = strip.trim_primer(self.primer, self.baseline,
                               self.min_primer_match, self.max_primer_offset)
   self.assertTrue(same_sequence(trimmed, self.baseline[:-len(self.primer)]),
       self.inequality_error.format(trimmed, self.baseline))

Example #5

File: strip_primer_tails_test.py Project: churchmanlab/NET-seq

 def testIgnoredShortPrimerTrimming(self):
   self.baseline = self.baseline[:-5] + self.primer_seq[:5]
   trimmed = strip.trim_primer(self.primer, self.baseline,
                               self.min_primer_match)
   self.assertTrue(same_sequence(trimmed, self.baseline),
       self.inequality_error.format(trimmed, self.baseline))