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#!/usr/bin/env python
"""Tests of code for aligning 16S sequences"""
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso","Jeremy Widmann"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from os import remove
from os.path import getsize
from cogent import LoadSeqs, DNA
from cogent.core.alignment import DenseAlignment, Alignment
from cogent.util.unit_test import TestCase, main
from qiime.util import get_tmp_filename
from qiime.align_seqs import (
Aligner, CogentAligner, PyNastAligner, InfernalAligner,
alignment_module_names,
)
def remove_files(list_of_filepaths,error_on_missing=True):
missing = []
for fp in list_of_filepaths:
try:
remove(fp)
except OSError:
missing.append(fp)
if error_on_missing and missing:
raise OSError, "Some filepaths were not accessible: %s" % '\t'.join(missing)
class AlignerTests(TestCase):
"""Tests of the abstract Aligner class"""
def test_init(self):
"""Abstract Aligner __init__ should store name, params"""
p = Aligner({})
self.assertEqual(p.Name, 'Aligner')
self.assertEqual(p.Params, {})
def test_call(self):
"""Abstract Aligner __call__ should raise NotImplementedError"""
p = Aligner({})
self.assertRaises(NotImplementedError, p, '/path/to/seqs')
class SharedSetupTestCase(TestCase):
"""Shared setup for aligner tests"""
def tearDown(self):
remove_files(self._paths_to_clean_up)
class CogentAlignerTests(SharedSetupTestCase):
"""Tests of the CogentAligner class"""
def setUp(self):
self.input_fp = get_tmp_filename(\
prefix='CogentAlignerTests_',suffix='.fasta')
open(self.input_fp,'w').write(seqs_for_muscle)
self._paths_to_clean_up =\
[self.input_fp]
self.muscle_module = alignment_module_names['muscle']
def test_call_correct_alignment(self):
"""CogentAligner: output expected alignment file
"""
p = CogentAligner({'Module': self.muscle_module})
log_fp = get_tmp_filename(\
prefix='CogentAlignerTests_',suffix='.log')
self._paths_to_clean_up.append(log_fp)
actual = p(result_path=None, seq_path=self.input_fp,
log_path=log_fp)
expected = expected_muscle_alignment
#note: lines in diff order w/ diff versions
self.assertEqualItems(str(actual).splitlines(),expected.splitlines())
def test_muscle_max_memory(self):
"""CogentAligner: muscle_max_memory should be passed to alignment fcn
"""
p = CogentAligner({
'Module': self.muscle_module,
'-maxmb': '200',
})
self.assertEqual(p.Params["-maxmb"], "200")
log_fp = get_tmp_filename(\
prefix='CogentAlignerTests_',suffix='.log')
self._paths_to_clean_up.append(log_fp)
actual = p(result_path=None, seq_path=self.input_fp,
log_path=log_fp)
expected = expected_muscle_alignment
#note: lines in diff order w/ diff versions
self.assertEqualItems(str(actual).splitlines(),expected.splitlines())
class InfernalAlignerTests(SharedSetupTestCase):
"""Tests of the InfernalAligner class"""
def setUp(self):
self.infernal_test1_input_fp = get_tmp_filename(
prefix='InfernalAlignerTests_',suffix='.fasta')
open(self.infernal_test1_input_fp,'w').write(infernal_test1_input_fasta)
self.infernal_test1_template_fp = get_tmp_filename(
prefix='InfernalAlignerTests_',suffix='template.sto')
open(self.infernal_test1_template_fp,'w').\
write(infernal_test1_template_stockholm)
# create temp file names (and touch them so we can reliably
# clean them up)
self.result_fp = get_tmp_filename(
prefix='InfernalAlignerTests_',suffix='.fasta')
open(self.result_fp,'w').close()
self.log_fp = get_tmp_filename(
prefix='InfernalAlignerTests_',suffix='.log')
open(self.log_fp,'w').close()
self._paths_to_clean_up = [
self.infernal_test1_input_fp,
self.result_fp,
self.log_fp,
self.infernal_test1_template_fp,
]
self.infernal_test1_aligner = InfernalAligner({
'template_filepath': self.infernal_test1_template_fp,
})
self.infernal_test1_expected_aln = \
LoadSeqs(data=infernal_test1_expected_alignment,aligned=Alignment,\
moltype=DNA)
def test_call_infernal_test1_file_output(self):
"""InfernalAligner writes correct output files for infernal_test1 seqs
"""
# do not collect results; check output files instead
actual = self.infernal_test1_aligner(\
self.infernal_test1_input_fp, result_path=self.result_fp,
log_path=self.log_fp)
self.assertTrue(actual == None,\
"Result should be None when result path provided.")
expected_aln = self.infernal_test1_expected_aln
actual_aln = LoadSeqs(self.result_fp,aligned=Alignment)
self.assertEqual(actual_aln,expected_aln)
def test_call_infernal_test1(self):
"""InfernalAligner: functions as expected when returing objects
"""
actual_aln = self.infernal_test1_aligner(self.infernal_test1_input_fp)
expected_aln = self.infernal_test1_expected_aln
expected_names = ['seq_1', 'seq_2', 'seq_3']
self.assertEqual(sorted(actual_aln.Names), expected_names)
self.assertEqual(actual_aln, expected_aln)
class PyNastAlignerTests(SharedSetupTestCase):
"""Tests of the PyNastAligner class"""
def setUp(self):
self.pynast_test1_input_fp = get_tmp_filename(
prefix='PyNastAlignerTests_',suffix='.fasta')
open(self.pynast_test1_input_fp,'w').write(pynast_test1_input_fasta)
self.pynast_test1_template_fp = get_tmp_filename(
prefix='PyNastAlignerTests_',suffix='template.fasta')
open(self.pynast_test1_template_fp,'w').\
write(pynast_test1_template_fasta)
self.pynast_test_template_w_dots_fp = get_tmp_filename(
prefix='PyNastAlignerTests_',suffix='template.fasta')
open(self.pynast_test_template_w_dots_fp,'w').\
write(pynast_test1_template_fasta.replace('-','.'))
self.pynast_test_template_w_u_fp = get_tmp_filename(
prefix='PyNastAlignerTests_',suffix='template.fasta')
open(self.pynast_test_template_w_u_fp,'w').\
write(pynast_test1_template_fasta.replace('T','U'))
self.pynast_test_template_w_lower_fp = get_tmp_filename(
prefix='PyNastAlignerTests_',suffix='template.fasta')
open(self.pynast_test_template_w_lower_fp,'w').\
write(pynast_test1_template_fasta.lower())
# create temp file names (and touch them so we can reliably
# clean them up)
self.result_fp = get_tmp_filename(
prefix='PyNastAlignerTests_',suffix='.fasta')
open(self.result_fp,'w').close()
self.failure_fp = get_tmp_filename(
prefix='PyNastAlignerTests_',suffix='.fasta')
open(self.failure_fp,'w').close()
self.log_fp = get_tmp_filename(
prefix='PyNastAlignerTests_',suffix='.log')
open(self.log_fp,'w').close()
self._paths_to_clean_up = [
self.pynast_test1_input_fp,
self.result_fp,
self.failure_fp,
self.log_fp,
self.pynast_test1_template_fp,
self.pynast_test_template_w_dots_fp,
self.pynast_test_template_w_u_fp,
self.pynast_test_template_w_lower_fp
]
self.pynast_test1_aligner = PyNastAligner({
'template_filepath': self.pynast_test1_template_fp,
'min_len': 15,
})
self.pynast_test1_expected_aln = \
LoadSeqs(data=pynast_test1_expected_alignment,aligned=DenseAlignment)
self.pynast_test1_expected_fail = \
LoadSeqs(data=pynast_test1_expected_failure,aligned=False)
def test_call_pynast_test1_file_output(self):
"""PyNastAligner writes correct output files for pynast_test1 seqs
"""
# do not collect results; check output files instead
actual = self.pynast_test1_aligner(\
self.pynast_test1_input_fp, result_path=self.result_fp,
log_path=self.log_fp, failure_path=self.failure_fp)
self.assertTrue(actual == None,\
"Result should be None when result path provided.")
expected_aln = self.pynast_test1_expected_aln
actual_aln = LoadSeqs(self.result_fp,aligned=DenseAlignment)
self.assertEqual(actual_aln,expected_aln)
actual_fail = LoadSeqs(self.failure_fp,aligned=False)
self.assertEqual(actual_fail.toFasta(),\
self.pynast_test1_expected_fail.toFasta())
def test_call_pynast_test1_file_output_alt_params(self):
"""PyNastAligner writes correct output files when no seqs align
"""
aligner = PyNastAligner({
'template_filepath': self.pynast_test1_template_fp,
'min_len':1000})
actual = aligner(\
self.pynast_test1_input_fp, result_path=self.result_fp,
log_path=self.log_fp, failure_path=self.failure_fp)
self.assertTrue(actual == None,\
"Result should be None when result path provided.")
self.assertEqual(getsize(self.result_fp),0,\
"No alignable seqs should result in an empty file.")
# all seqs reported to fail
actual_fail = LoadSeqs(self.failure_fp,aligned=False)
self.assertEqual(actual_fail.getNumSeqs(),3)
def test_call_pynast_test1(self):
"""PyNastAligner: functions as expected when returing objects
"""
actual_aln = self.pynast_test1_aligner(self.pynast_test1_input_fp)
expected_aln = self.pynast_test1_expected_aln
expected_names = ['1 description field 1..23', '2 1..23']
self.assertEqual(actual_aln.Names, expected_names)
self.assertEqual(actual_aln, expected_aln)
def test_call_pynast_template_aln_with_dots(self):
"""PyNastAligner: functions when template alignment contains dots
"""
pynast_aligner = PyNastAligner({
'template_filepath': self.pynast_test_template_w_dots_fp,
'min_len': 15,
})
actual_aln = pynast_aligner(self.pynast_test1_input_fp)
expected_aln = self.pynast_test1_expected_aln
expected_names = ['1 description field 1..23', '2 1..23']
self.assertEqual(actual_aln.Names, expected_names)
self.assertEqual(actual_aln, expected_aln)
def test_call_pynast_template_aln_with_lower(self):
"""PyNastAligner: functions when template alignment contains lower case
"""
pynast_aligner = PyNastAligner({
'template_filepath': self.pynast_test_template_w_lower_fp,
'min_len': 15,
})
actual_aln = pynast_aligner(self.pynast_test1_input_fp)
expected_aln = self.pynast_test1_expected_aln
expected_names = ['1 description field 1..23', '2 1..23']
self.assertEqual(actual_aln.Names, expected_names)
self.assertEqual(actual_aln, expected_aln)
def test_call_pynast_template_aln_with_U(self):
"""PyNastAligner: error message when template contains bad char
"""
pynast_aligner = PyNastAligner({
'template_filepath': self.pynast_test_template_w_u_fp,
'min_len': 15,
})
self.assertRaises(KeyError,pynast_aligner,self.pynast_test1_input_fp)
def test_call_pynast_alt_pairwise_method(self):
"""PyNastAligner: alternate pairwise alignment method produces correct alignment
"""
aligner = PyNastAligner({
'pairwise_alignment_method': 'muscle',
'template_filepath': self.pynast_test1_template_fp,
'min_len': 15,
})
actual_aln = aligner(self.pynast_test1_input_fp)
expected_aln = self.pynast_test1_expected_aln
self.assertEqual(actual_aln, expected_aln)
def test_call_pynast_test1_alt_min_len(self):
"""PyNastAligner: returns no result when min_len too high
"""
aligner = PyNastAligner({
'template_filepath': self.pynast_test1_template_fp,
'min_len':1000})
actual_aln = aligner(\
self.pynast_test1_input_fp)
expected_aln = {}
self.assertEqual(actual_aln, expected_aln)
def test_call_pynast_test1_alt_min_pct(self):
"""PyNastAligner: returns no result when min_pct too high
"""
aligner = PyNastAligner({
'template_filepath': self.pynast_test1_template_fp,
'min_len':15,
'min_pct':100.0})
actual_aln = aligner(self.pynast_test1_input_fp)
expected_aln = {}
self.assertEqual(actual_aln, expected_aln)
def tearDown(self):
"""
"""
remove_files(self._paths_to_clean_up)
seqs_for_muscle= \
""">abc
ACACACAC
>def
ACAGACAC
>ghi
ACAGACACTT
>jkl
TTACAC"""
expected_muscle_alignment = """>jkl\n--TTACAC--\n>abc\nACACACAC--\n>ghi\nACAGACACTT\n>def\nACAGACAC--\n"""
infernal_test1_input_fasta = """>seq_1
ACTGCTAGCTAGTAGCGTACGTA
>seq_2
GCTACGTAGCTAC
>seq_3
GCGGCTATTAGATCGTA"""
infernal_test1_template_stockholm = """# STOCKHOLM 1.0
seq_a TAGGCTCTGATATAATAGC-TCTC---------
seq_b ----TATCGCTTCGACGAT-TCTCTGATAGAGA
seq_c ------------TGACTAC-GCAT---------
#=GC SS_cons ............((.(....)))..........
//"""
infernal_test1_expected_alignment = """>seq_1
-----ACTGCTA-GCTAGTAGCGTACGTA----
>seq_2
--------GCTACG-TAGCTAC-----------
>seq_3
-----GCGGCTATTAGATC-GTA----------
"""
pynast_test1_template_fasta = """>1
ACGT--ACGTAC-ATA-C-----CC-T-G-GTA-G-T---
>2
AGGTTTACGTAG-ATA-C-----CC-T-G-GTA-G-T---
>3
AGGTACT-CCAC-ATA-C-----CC-T-G-GTA-G-T---
>4
TCGTTCGT-----ATA-C-----CC-T-G-GTA-G-T---
>5
ACGTACGT-TA--ATA-C-----CC-T-G-GTA-G-T---
"""
pynast_test1_input_fasta = """>1 description field
ACCTACGTTAATACCCTGGTAGT
>2
ACCTACGTTAATACCCTGGTAGT
>3
AA
"""
pynast_test1_expected_alignment = """>1 description field 1..23
ACCTACGT-TA--ATA-C-----CC-T-G-GTA-G-T---
>2 1..23
ACCTACGT-TA--ATA-C-----CC-T-G-GTA-G-T---
"""
pynast_test1_expected_failure = """>3
AA
"""
#run unit tests if run from command-line
if __name__ == '__main__':
main()
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