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test_filter_alignment.py
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test_filter_alignment.py
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#!/usr/bin/env python
__author__ = "Dan Knights"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso","Dan Knights"]
__license__ = "GPL"
__version__ = "1.3.0"
__maintainer__ = "Dan Knights"
__email__ = "danknights@gmail.com"
__status__ = "Release"
from numpy import array
from cogent.util.unit_test import TestCase, main
from cogent import LoadSeqs
from qiime.filter_alignment import apply_lane_mask, apply_gap_filter,\
apply_lane_mask_and_gap_filter, remove_outliers, freqs_from_aln_array,\
generate_lane_mask
class FilterAlignmentTests(TestCase):
def setUp(self):
"""Init variables for the tests """
self.aln1 = [\
'>s1','ACC--T',\
'>s2','AC---T',\
'>s3','TCT--T',\
'>s4','ACG--T',\
'>s5','---A--'\
]
self.aln2 = aln2_fasta.split('\n')
self.aln2_lm = aln2_lm
def test_apply_lane_mask_and_gap_filter_real(self):
"""apply_lane_mask_and_gap_filter: no error on full length seqs
"""
# No error when applying to full-length sequence
actual = apply_lane_mask_and_gap_filter(\
self.aln2,self.aln2_lm)
def test_apply_lane_mask_and_gap_filter(self):
"""apply_lane_mask_and_gap_filter: functions as expected
"""
lm = '111111'
expected = self.aln1.__iter__()
for result in apply_lane_mask_and_gap_filter(self.aln1,lm,1.0):
self.assertEqual(result,expected.next()+'\n')
lm = None
expected = self.aln1.__iter__()
for result in apply_lane_mask_and_gap_filter(self.aln1,lm,1.0):
self.assertEqual(result,expected.next()+'\n')
# gap filter only
lm = '111111'
expected = [\
'>s1','ACC-T',\
'>s2','AC--T',\
'>s3','TCT-T',\
'>s4','ACG-T',\
'>s5','---A-'\
].__iter__()
for result in apply_lane_mask_and_gap_filter(self.aln1,lm):
self.assertEqual(result,expected.next()+'\n')
# lm filter only
lm = '011111'
expected = [\
'>s1','CC--T',\
'>s2','C---T',\
'>s3','CT--T',\
'>s4','CG--T',\
'>s5','--A--'\
].__iter__()
for result in apply_lane_mask_and_gap_filter(self.aln1,lm,1.0):
self.assertEqual(result,expected.next()+'\n')
# gap and lm filter
lm = '011111'
expected = [\
'>s1','CC-T',\
'>s2','C--T',\
'>s3','CT-T',\
'>s4','CG-T',\
'>s5','--A-'\
].__iter__()
for result in apply_lane_mask_and_gap_filter(self.aln1,lm):
self.assertEqual(result,expected.next()+'\n')
def test_apply_lane_mask(self):
""" apply_lane_mask: functions as expected with varied lane masks
"""
lm1 = '111111'
expected = self.aln1.__iter__()
for result in apply_lane_mask(self.aln1,lm1):
self.assertEqual(result,expected.next()+'\n')
lm2 = '000000'
expected = [\
'>s1','',\
'>s2','',\
'>s3','',\
'>s4','',\
'>s5',''\
].__iter__()
for result in apply_lane_mask(self.aln1,lm2):
self.assertEqual(result,expected.next()+'\n')
lm3 = '101010'
expected = [\
'>s1','AC-',\
'>s2','A--',\
'>s3','TT-',\
'>s4','AG-',\
'>s5','---'\
].__iter__()
for result in apply_lane_mask(self.aln1,lm3):
self.assertEqual(result,expected.next()+'\n')
lm4 = '000111'
expected = [\
'>s1','--T',\
'>s2','--T',\
'>s3','--T',\
'>s4','--T',\
'>s5','A--'\
].__iter__()
for result in apply_lane_mask(self.aln1,lm4):
self.assertEqual(result,expected.next()+'\n')
def test_apply_gap_filter(self):
""" apply_gap_filter: functions as expected with varied allowed_gap_frac
"""
expected = self.aln1.__iter__()
for result in apply_gap_filter(self.aln1,1.0):
self.assertEqual(result,expected.next()+'\n')
expected = [\
'>s1','ACC-T',\
'>s2','AC--T',\
'>s3','TCT-T',\
'>s4','ACG-T',\
'>s5','---A-'\
].__iter__()
for result in apply_gap_filter(self.aln1):
self.assertEqual(result,expected.next()+'\n')
expected = [\
'>s1','ACCT',\
'>s2','AC-T',\
'>s3','TCTT',\
'>s4','ACGT',\
'>s5','----'\
].__iter__()
for result in apply_gap_filter(self.aln1,0.75):
self.assertEqual(result,expected.next()+'\n')
expected = [\
'>s1','ACCT',\
'>s2','AC-T',\
'>s3','TCTT',\
'>s4','ACGT',\
'>s5','----'\
].__iter__()
for result in apply_gap_filter(self.aln1,0.40):
self.assertEqual(result,expected.next()+'\n')
expected = [\
'>s1','ACT',\
'>s2','ACT',\
'>s3','TCT',\
'>s4','ACT',\
'>s5','---'\
].__iter__()
for result in apply_gap_filter(self.aln1,0.30):
self.assertEqual(result,expected.next()+'\n')
expected = [\
'>s1','',\
'>s2','',\
'>s3','',\
'>s4','',\
'>s5',''\
].__iter__()
for result in apply_gap_filter(self.aln1,0.10):
self.assertEqual(result,expected.next()+'\n')
# the following tests were adapted from test_alignment.py in PyCogent
aln = [\
'>a','--A-BC-',\
'>b','-CB-A--',\
'>c','--D-EF-'\
]
#default should strip out cols that are 100% gaps
expected = [\
'>a','-ABC',\
'>b','CBA-',\
'>c','-DEF'\
].__iter__()
for result in apply_gap_filter(aln):
self.assertEqual(result,expected.next()+'\n')
# if allowed_gap_frac is 1, shouldn't delete anything
expected = [\
'>a','--A-BC-',\
'>b','-CB-A--',\
'>c','--D-EF-'\
].__iter__()
for result in apply_gap_filter(aln,1):
self.assertEqual(result,expected.next()+'\n')
#if allowed_gap_frac is 0, should strip out any cols containing gaps
expected = [\
'>a','AB',\
'>b','BA',\
'>c','DE'\
].__iter__()
for result in apply_gap_filter(aln,0):
self.assertEqual(result,expected.next()+'\n')
#intermediate numbers should work as expected
expected = [\
'>a','ABC',\
'>b','BA-',\
'>c','DEF'\
].__iter__()
for result in apply_gap_filter(aln,0.4):
self.assertEqual(result,expected.next()+'\n')
expected = [\
'>a','-ABC',\
'>b','CBA-',\
'>c','-DEF'\
].__iter__()
for result in apply_gap_filter(aln,0.7):
self.assertEqual(result,expected.next()+'\n')
def test_apply_lane_mask_and_gap_filter_alternate_alignment(self):
"""apply_lane_mask_and_gap_filter: functions as expected with alt aln
"""
aln = [\
'>ACT009','AACT-',\
'>ACT019','AACT-',\
'>ACT011','-TCT-'\
]
expected = aln.__iter__()
for result in apply_lane_mask_and_gap_filter(aln,None,1.0):
self.assertEqual(result,expected.next()+'\n')
lm = '00111'
expected = [\
'>ACT009','CT',\
'>ACT019','CT',\
'>ACT011','CT'\
].__iter__()
for result in apply_lane_mask_and_gap_filter(aln,lm):
self.assertEqual(result,expected.next()+'\n')
def test_remove_outliers(self):
""" remove outliers returns only seqs similar to consensus"""
aln = [\
'>ACT009','ACAT-',
'>ACT019','GACT-',
'>ACT_02','GACT-',
'>ACT_03','AACT-',
'>ACT_04','AACT-',
'>ACT_05','AACT-',
'>ACT011','CTGGC',
'>hello', 'AACTG',
]
# mean errors is 10/9 .
seqnames = []
for elem in aln:
if elem.startswith('>'):
seqnames.append (elem[1:])
seqs = []
for elem in aln:
if not elem.startswith('>'):
seqs.append(elem)
# just remove ACT011
res = remove_outliers(aln, 2)
self.assertEqual(len(res.getSeqNames()), 7)
for seqname_left in res.getSeqNames():
self.assertContains(seqnames, seqname_left)
self.assertNotContains(res.getSeqNames(), 'ACT011')
# now remove all that deviate have > 10/9 (2 or more) substitutions:
res = remove_outliers(aln, 0)
self.assertEqual(len(res.getSeqNames()), 6)
for seqname_left in res.getSeqNames():
self.assertContains(seqnames, seqname_left)
self.assertNotContains(res.getSeqNames(), 'ACT011')
self.assertNotContains(res.getSeqNames(), 'ACT009')
def test_generate_lane_mask(self):
""" Generates correct lane mask for dynamic entropy filtering """
sample_alignment = """>1
.ATC-G
>2
.AACCG
>3
.ATC-G
>4
.AAC-G""".split('\n')
entropy_threshold = 0.70
expected_lanemask = "110101"
actual_lanemask = generate_lane_mask(sample_alignment,
entropy_threshold)
self.assertEqual(actual_lanemask, expected_lanemask)
def test_freqs_from_aln_array(self):
""" Returns positional frequences from alignments correctly """
sample_alignment = """>1
.ATC-G
>2
.AACCG
>3
.ATC-G
>4
.AAC-G""".split('\n')
results = freqs_from_aln_array(sample_alignment).Data
t_index = 0
c_index = 1
a_index = 2
g_index = 3
gap_index = 4
t_expected = array([0,0,2,0,0,0])
c_expected = array([0,0,0,4,1,0])
a_expected = array([0,4,2,0,0,0])
g_expected = array([0,0,0,0,0,4])
gap_expected = array([4,0,0,0,3,0])
self.assertEqual(results[t_index], t_expected)
self.assertEqual(results[c_index], c_expected)
self.assertEqual(results[a_index], a_expected)
self.assertEqual(results[g_index], g_expected)
self.assertEqual(results[gap_index], gap_expected)
aln2_fasta = """>1121 HalF20SW_57886 RC:1..219
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A--AT-GT-A-T-A-GT---TAA--T-CT-G--C-C-CCA--TA-G------------------------------------------------------------------T-GG----AGG-AC-AA-CAG-------------------------T-T-A-----------------------GAA-A---TGA-CTG-CTAA-TA---CT-C--C-AT-A----------C--------------------T-C--C-T-T--C--T-----------------T----AT-C-----------------------------------------------------------------------------------------------------------------------A-TA-A--------------------------------------------------------------------------------------------------------------------------------------G-T-T----A---------------A--G-T-C-G-G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAA--G-T----------------------------------------------------------------------------------------------------------------------------------------TTT------------------------------------------------------------------------------------------------------------------------------------T---C-G--------------C----T-A---T-GG-G---AT---G-A-----G-ACT-ATA--T-CGT--A------TC--A--G-CT-A----G---TTGG-T-A-AG-G-T----AAT-GG-C-T-T-ACCA--A-GG-C-T--A-TG-A------------CGC-G-T------AA-CT-G-G-TCT-G-AG----A--GG-AT--G-AT-C-AG-TCAC-A-TTGGA--A-C-TG-A-GA-C-AC-G-G-TCCAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>1122 HalF02FT_61708 RC:7..217
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G--C-C-TGG--TA-G------------------------------------------------------------------T-GG----GGG-AT-AA-CTA-------------------------T-T-G-----------------------GAA-A---CGA-TAG-CTAA-TA---CC-G--C-AT-A---------------------------------A-TA-G-C--A--G-----------------TT---GT-T-----------------------------------------------------------------------------------------------------------------------G-CA-T--------------------------------------------------------------------------------------------------------------------------------------G-A-C--A-A---------------C--T-G-T-T-T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAA--G-G-T-GC-----------------------------------------------------------------------------------------------------------------------------------AAT-T----------------------------------------------------------------------------------------------------------------------------G-CA--C---C-A--------------C----T-A---C-CA-G---AT---G-G-----A-CCT-GCG--T-TGT--A------TT--A--G-CT-A----G---TTGG-T-G-GG-G-T----AAC-GG-C-T-C-ACCA--A-GG-C-G--A-CG-A------------TAC-A-T------AG-CC-G-A-CCT-G-AG----A--GG-GT--G-AT-C-GG-CCAC-A-CTGGG--A-C-TG-A-GA-C-AC-G-G-CCCAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"""
aln2_lm = 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if __name__ == "__main__":
main()