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test_truncate_reverse_primer.py
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test_truncate_reverse_primer.py
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#!/usr/bin/env python
# File created February 29, 2012
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters"]
__license__ = "GPL"
__version__ = "1.9.0"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import exists, join, basename
from os import close
from shutil import rmtree
from tempfile import mkdtemp, mkstemp
from unittest import TestCase, main
from qiime.util import create_dir
from skbio.util import remove_files
from qiime.truncate_reverse_primer import get_rev_primer_seqs,\
get_output_filepaths, truncate_rev_primers, truncate_reverse_primer
from skbio.sequence import BiologicalSequenceError
class FakeOutFile(object):
def __init__(self):
self.data = ""
def write(self, s):
self.data += s
class TruncateRemoveReversePrimerTests(TestCase):
""" Unit tests for the truncate_reverse_primers.py module """
def setUp(self):
# create the temporary input files that will be used
self._files_to_remove = []
self.sample_fasta_file1_data = sample_fasta_file1
self.sample_fasta_file_bad_labels_data =\
sample_fasta_file_bad_labels
self.sample_mapping_file1_data = sample_mapping_file1
self.sample_mapping_file_no_revprimer_header =\
sample_mapping_file_no_revprimer_header
self.sample_mapping_file_bad_revprimer =\
sample_mapping_file_bad_revprimer
self.expected_truncation_default_settings =\
expected_truncation_default_settings
self.expected_truncation_zero_mismatches =\
expected_truncation_zero_mismatches
self.expected_truncation_zero_mismatches_truncate_remove =\
expected_truncation_zero_mismatches_truncate_remove
fd, self.fasta_fp = mkstemp(prefix='fasta_seqs_',
suffix='.fna')
close(fd)
seq_file = open(self.fasta_fp, 'w')
seq_file.write(self.sample_fasta_file1_data)
seq_file.close()
fd, self.fasta_badlabels_fp = mkstemp(prefix="fasta_seqs_badlabels_",
suffix=".fna")
close(fd)
seq_file = open(self.fasta_badlabels_fp, "w")
seq_file.write(self.sample_fasta_file_bad_labels_data)
seq_file.close()
fd, self.mapping_fp = mkstemp(prefix='sample_mapping_',
suffix='.txt')
close(fd)
mapping_file = open(self.mapping_fp, "w")
mapping_file.write(self.sample_mapping_file1_data)
mapping_file.close()
fd, self.mapping_bad_header_fp = mkstemp(
prefix='sample_mapping_badheader_',
suffix=".txt")
close(fd)
mapping_file = open(self.mapping_bad_header_fp, "w")
mapping_file.write(self.sample_mapping_file_no_revprimer_header)
mapping_file.close()
fd, self.mapping_bad_primer_fp = mkstemp(
prefix='sample_mapping_badprimer_',
suffix=".txt")
close(fd)
mapping_file = open(self.mapping_bad_primer_fp, "w")
mapping_file.write(self.sample_mapping_file_bad_revprimer)
mapping_file.close()
self.output_dir = mkdtemp()
self.output_dir += '/'
create_dir(self.output_dir)
self._files_to_remove =\
[self.fasta_fp, self.mapping_fp, self.mapping_bad_header_fp,
self.mapping_bad_primer_fp, self.fasta_badlabels_fp]
def tearDown(self):
if self._files_to_remove:
remove_files(self._files_to_remove)
if exists(self.output_dir):
rmtree(self.output_dir)
def test_get_rev_primer_seqs(self):
""" Builds dict of reverse primers from mapping file """
actual_rev_primers = get_rev_primer_seqs(open(self.mapping_fp, "U"))
expected_rev_primers = {'PC.481': ['CTCTCCG'], 'PC.634': ['CTCTCAG'],
'PC.635': ['CTCTCAG'], 'PC.636': ['CTCTCAG'], 'PC.354': ['CTCTCAG',
'TTCTCRG']}
self.assertEqual(actual_rev_primers, expected_rev_primers)
def test_get_rev_primer_seqs_errors(self):
"""Raises errors with invalid mapping file """
# Raises error if missing ReversePrimer column
with open(self.mapping_bad_header_fp, "U") as f:
self.assertRaises(KeyError, get_rev_primer_seqs, f)
# Raises error if invalid characters in primer
with open(self.mapping_bad_primer_fp, "U") as f:
self.assertRaises(BiologicalSequenceError, get_rev_primer_seqs, f)
def test_get_output_filepaths(self):
""" Properly returns output filepaths """
actual_fna_fp, actual_log_fp = get_output_filepaths(".",
'/home/tests/seqs.fna')
expected_fna_fp = "./seqs_rev_primer_truncated.fna"
expected_log_fp = "./rev_primer_truncation.log"
self.assertEqual(actual_fna_fp, expected_fna_fp)
self.assertEqual(actual_log_fp, expected_log_fp)
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_reverse_primer(self):
""" Overall module functionality test """
truncate_reverse_primer(self.fasta_fp, self.mapping_fp,
self.output_dir, truncate_option='truncate_only', primer_mismatches=2)
output_log_fp = open(join(self.output_dir,
"rev_primer_truncation.log"), "U")
actual_log_lines = [line.strip() for line in output_log_fp]
# Because filepaths used are recorded, need the tmp filepaths
expected_log_lines = ['Details for removal of reverse primers',
'Original fasta filepath: %s' % self.fasta_fp,
'Total seqs in fasta: 6',
'Mapping filepath: %s' % self.mapping_fp,
'Truncation option: truncate_only',
'Mismatches allowed: 2',
'Total seqs written: 5',
'SampleIDs not found: 0',
'Reverse primers not found: 0']
self.assertEqual(actual_log_lines, expected_log_lines)
expected_fna_fp = basename(self.fasta_fp.replace('.fna', '')) +\
"_rev_primer_truncated.fna"
fasta_fp = open(join(self.output_dir, expected_fna_fp), "U")
actual_fasta_output = [line.strip() for line in fasta_fp]
self.assertEqual(actual_fasta_output,
self.expected_truncation_default_settings.strip().split('\n'))
sample_fasta_file1 = """>PC.634_1 FLP3FBN01ELBSX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACCCTCTCAGGCCGGCTAC
>PC.634_2 FLP3FBN01EG8AX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
TTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCCCTCTCAGAACCCCTATC
>PC.354_3 FLP3FBN01EEWKD orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0
TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTTAACTCGGCTAT
>PC.481_4 FLP3FBN01DEHK3 orig_bc=ACCAGCGACTAG new_bc=ACCAGCGACTAG bc_diffs=0
CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTAC
>PC.634_5 FLP3FBN01DGFYQ orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTAC
>PC.634_6 RevPrimerAtStart FLP3FBN01DGFYQ orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
CTCTCAGCACCGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACC
"""
sample_fasta_file_bad_labels = """>CaptHammer_1 FLP3FBN01ELBSX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACCCTCTCAGGCCGGCTAC
>JohnnySnow_2 FLP3FBN01EG8AX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
TTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCCCTCTCAGAACCCCTATC
>BadHorse_3 FLP3FBN01EEWKD orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0
TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTTAACTCGGCTAT
>Moist_4 FLP3FBN01DEHK3 orig_bc=ACCAGCGACTAG new_bc=ACCAGCGACTAG bc_diffs=0
CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTAC
>DrHorrible_5 FLP3FBN01DGFYQ orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTAC
"""
expected_truncation_default_settings = """>PC.634_1 FLP3FBN01ELBSX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACC
>PC.634_2 FLP3FBN01EG8AX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
TTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCC
>PC.354_3 FLP3FBN01EEWKD orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0
TTGGGCCGT
>PC.481_4 FLP3FBN01DEHK3 orig_bc=ACCAGCGACTAG new_bc=ACCAGCGACTAG bc_diffs=0
CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAAC
>PC.634_5 FLP3FBN01DGFYQ orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACC
"""
expected_truncation_zero_mismatches = """>PC.634_1 FLP3FBN01ELBSX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACC
>PC.634_2 FLP3FBN01EG8AX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
TTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCC
>PC.354_3 FLP3FBN01EEWKD orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0
TTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTTAACTCGGCTAT
>PC.481_4 FLP3FBN01DEHK3 orig_bc=ACCAGCGACTAG new_bc=ACCAGCGACTAG bc_diffs=0
CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTAC
>PC.634_5 FLP3FBN01DGFYQ orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACC
"""
expected_truncation_zero_mismatches_truncate_remove = """>PC.634_1 FLP3FBN01ELBSX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
CTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACC
>PC.634_2 FLP3FBN01EG8AX orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
TTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCC
>PC.634_5 FLP3FBN01DGFYQ orig_bc=ACAGAGTCGGCT new_bc=ACAGAGTCGGCT bc_diffs=0
TTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACC
"""
sample_mapping_file1 = """#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB ReversePrimer Description
"#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009)."
PC.354 AGCACGAGCCTA YATGCTGCCTCCCGTAGGAGT Control 20061218 CTGAGAG,CYGAGAA Control_mouse_I.D._354
PC.481 ACCAGCGACTAG YATGCTGCCTCCCGTAGGAGT Control 20070314 CGGAGAG Control_mouse_I.D._481
PC.634 ACAGAGTCGGCT &&&YATGCTGCCTCCCGTAGGAGT Fast 20080116 CTGAGAG Fasting_mouse_I.D._634
PC.635 ACCGCAGAGTCA YATGCTGCCTCCCGTAGGAGT Fast 20080116 CTGAGAG Fasting_mouse_I.D._635
PC.636 ACGGTGAGTGTC YATGCTGCCTCCCGTAGGAGT Fast 20080116 CTGAGAG Fasting_mouse_I.D._636"""
sample_mapping_file_no_revprimer_header = """#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB XXXX Description
"#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009)."
PC.354 AGCACGAGCCTA YATGCTGCCTCCCGTAGGAGT Control 20061218 CTGAGAG Control_mouse_I.D._354
PC.481 ACCAGCGACTAG YATGCTGCCTCCCGTAGGAGT Control 20070314 CGGAGAG Control_mouse_I.D._481
PC.634 ACAGAGTCGGCT YATGCTGCCTCCCGTAGGAGT Fast 20080116 CTGAGAG Fasting_mouse_I.D._634
PC.635 ACCGCAGAGTCA YATGCTGCCTCCCGTAGGAGT Fast 20080116 CTGAGAG Fasting_mouse_I.D._635
PC.636 ACGGTGAGTGTC YATGCTGCCTCCCGTAGGAGT Fast 20080116 CTGAGAG Fasting_mouse_I.D._636"""
sample_mapping_file_bad_revprimer = """#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB ReversePrimer Description
"#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009)."
PC.354 AGCACGAGCCTA YATGCTGCCTCCCGTAGGAGT Control 20061218 CTGAGAG Control_mouse_I.D._354
PC.481 ACCAGCGACTAG YATGCTGCCTCCCGTAGGAGT Control 20070314 CGGAGAG Control_mouse_I.D._481
PC.634 ACAGAGTCGGCT YATGCTGCCTCCCGTAGGAGT Fast 20080116 CTGAGAG Fasting_mouse_I.D._634
PC.635 ACCGCAGAGTCA YATGCTGCCTCCCGTAGGAGT Fast 20080116 CTGAGXG Fasting_mouse_I.D._635
PC.636 ACGGTGAGTGTC YATGCTGCCTCCCGTAGGAGT Fast 20080116 CTGAGAG Fasting_mouse_I.D._636"""
if __name__ == '__main__':
main()