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#!/usr/bin/env python
# File created on 18 May 2010
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from cogent.util.unit_test import TestCase, main
from cogent.parse.tree import DndParser
from qiime.parse import parse_otu_table, parse_distmat
from qiime.filter import (filter_fasta,
filter_otus_from_otu_table,
filter_samples_from_otu_table,
filter_otu_table_to_n_samples,
filter_samples_from_distance_matrix,
split_otu_table_on_taxonomy,
negate_tips_to_keep)
class fake_output_f():
def __init__(self):
self.s = ""
def write(self,s):
self.s += s
def close(self):
pass
class FilterTests(TestCase):
def setUp(self):
self.filter_fasta_expected1 = filter_fasta_expected1
self.filter_fasta_expected2 = filter_fasta_expected2
self.input_otu_table1 = input_otu_table1.split('\n')
self.input_seqs_to_discard1 = input_seqs_to_discard1.split('\n')
self.expected_otu_table1a = expected_otu_table1a.split('\n')
self.expected_otu_table1b = expected_otu_table1b.split('\n')
self.expected_otu_table1c = expected_otu_table1c.split('\n')
self.expected_otu_table1d = expected_otu_table1d.split('\n')
self.input_dm1 = input_dm1.split('\n')
self.expected_dm1a = expected_dm1a.split('\n')
self.expected_dm1b = expected_dm1b.split('\n')
# split otu table test data
self.input_otu_table2 = input_otu_table2.split('\n')
self.input_otu_table2_bacteria = str(bacteria_otu_table1)
self.input_otu_table2_none = str(none_otu_table1)
self.input_otu_table2_archaea = str(archaea_otu_table1)
self.input_otu_table2_firmicutes = str(firmicutes_otu_table1)
self.input_otu_table2_bacteroidetes = str(bacteroidetes_otu_table1)
self.input_otu_table2_none_no_l2 = str(none_no_l2_otu_table1)
self.input_otu_table2_none_firmicutes = str(none_firmicutes_otu_table1)
def tearDown(self):
pass
def test_negate_tips_to_keep(self):
""" negate_tips_to_keep functions as expected """
t = DndParser("((S5:0.00014,S7:0.00015)0.752:0.45762,(S3:0.00014,"
"seq6:0.00014)0.180:0.00015,(Seq1:0.00014,s2:0.00014)0.528:1.0466);")
tips_to_keep = ["S5","Seq1","s2"]
expected = ["S7","S3","seq6"]
self.assertEqualItems(negate_tips_to_keep(tips_to_keep,t),expected)
tips_to_keep = ["S5","Seq1"]
expected = ["S7","S3","seq6","s2"]
self.assertEqualItems(negate_tips_to_keep(tips_to_keep,t),expected)
tips_to_keep = []
expected = ["S7","S3","seq6","s2","S5","Seq1"]
self.assertEqualItems(negate_tips_to_keep(tips_to_keep,t),expected)
tips_to_keep = ["S7","S3","seq6","s2","S5","Seq1"]
expected = []
self.assertEqualItems(negate_tips_to_keep(tips_to_keep,t),expected)
def test_split_otu_table_on_taxonomy(self):
""" splitting OTU table on taxonomy functions as expected
"""
# Level 1
actual = list(split_otu_table_on_taxonomy(
self.input_otu_table2,1))
actual.sort()
expected = [('Bacteria',self.input_otu_table2_bacteria),
('None',self.input_otu_table2_none),
('Archaea',self.input_otu_table2_archaea)]
expected.sort()
self.assertEqual(actual,expected)
# Level 2
actual = list(split_otu_table_on_taxonomy(
self.input_otu_table2,2))
actual.sort()
expected = [('Bacteria;Bacteroidetes',self.input_otu_table2_bacteroidetes),
('Bacteria;Firmicutes',self.input_otu_table2_firmicutes),
('None',self.input_otu_table2_none_no_l2),
('None;Firmicutes',self.input_otu_table2_none_firmicutes),
('Archaea',self.input_otu_table2_archaea)]
expected.sort()
self.assertEqual(actual,expected)
def test_filter_fasta(self):
"""filter_fasta functions as expected """
input_seqs = [('Seq1 some comment','ACCTTGG'),
('s2 some other comment','TTGG'),
('S3','AAGGCCGG'),
('S5 some comment','CGT'),
('seq6 some other comment','AA'),
('S7','T')]
seqs_to_keep = {}.fromkeys(['Seq1',
's2 some other comment',
'S3 no comment'])
actual = fake_output_f()
filter_fasta(input_seqs,
actual,
seqs_to_keep,
negate=False)
self.assertEqual(actual.s,self.filter_fasta_expected1)
actual = fake_output_f()
filter_fasta(input_seqs,
actual,
seqs_to_keep,
negate=True)
self.assertEqual(actual.s,self.filter_fasta_expected2)
def test_filter_otus_from_otu_table(self):
"""filter_otus_from_otu_table: functions as expected
"""
actual = filter_otus_from_otu_table(self.input_otu_table1,
self.input_seqs_to_discard1)
self.assertEqual(actual,self.expected_otu_table1a)
def test_filter_otus_from_otu_table_negate(self):
"""filter_otus_from_otu_table: functions as expected with negate=True
"""
actual = filter_otus_from_otu_table(self.input_otu_table1,
self.input_seqs_to_discard1,
negate=True)
self.assertEqual(actual,self.expected_otu_table1b)
def test_filter_samples_from_otu_table(self):
"""filter_samples_from_otu_table functions as expected """
actual = filter_samples_from_otu_table(self.input_otu_table1,
["DEF","GHI tfasd"])
self.assertEqual(actual,self.expected_otu_table1c)
# order of otu table is retained regardless of samples_to_keep order
actual = filter_samples_from_otu_table(self.input_otu_table1,
["XYZ"])
self.assertEqual(actual,self.expected_otu_table1d)
def test_filter_samples_from_otu_table_negate(self):
"""filter_samples_from_otu_table functions w negate """
actual = filter_samples_from_otu_table(self.input_otu_table1,
["ABC blah","XYZ"],
negate=True)
self.assertEqual(actual,self.expected_otu_table1c)
def test_filter_otu_table_to_n_samples(self):
"""filter_otu_table_to_n_samples functions as expected """
def check_no_zero_count_otus(data,otu_ids):
for d,id_ in zip(data,otu_ids):
self.assertTrue(sum(d)>0,
"OTU (%s) with total count=0 not " % id_ +\
"filtered from OTU table.")
actual = filter_otu_table_to_n_samples(self.input_otu_table1,1)
sample_ids,otu_ids,data,taxa = parse_otu_table(actual)
self.assertTrue(len(sample_ids),1)
check_no_zero_count_otus(data,otu_ids)
actual = filter_otu_table_to_n_samples(self.input_otu_table1,2)
sample_ids,otu_ids,data,taxa = parse_otu_table(actual)
self.assertTrue(len(sample_ids),2)
check_no_zero_count_otus(data,otu_ids)
actual = filter_otu_table_to_n_samples(self.input_otu_table1,3)
sample_ids,otu_ids,data,taxa = parse_otu_table(actual)
self.assertTrue(len(sample_ids),3)
check_no_zero_count_otus(data,otu_ids)
actual = filter_otu_table_to_n_samples(self.input_otu_table1,4)
sample_ids,otu_ids,data,taxa = parse_otu_table(actual)
self.assertTrue(len(sample_ids),4)
self.assertEqualItems(sample_ids,["ABC","DEF","GHI","XYZ"])
self.assertEqual(data.shape,(4,4))
check_no_zero_count_otus(data,otu_ids)
actual = filter_otu_table_to_n_samples(self.input_otu_table1,5)
sample_ids,otu_ids,data,taxa = parse_otu_table(actual)
self.assertTrue(len(sample_ids),4)
self.assertEqualItems(sample_ids,["ABC","DEF","GHI","XYZ"])
self.assertEqual(data.shape,(4,4))
check_no_zero_count_otus(data,otu_ids)
# different samples selected on different runs
r = []
for i in range(25):
actual = filter_otu_table_to_n_samples(self.input_otu_table1,1)
sample_ids,otu_ids,data,taxa = parse_otu_table(actual)
r.append(tuple(sample_ids))
self.assertTrue(len({}.fromkeys(r)) > 1)
def test_filter_otu_table_to_n_samples_handles_bad_n(self):
"""filter_otu_table_to_n_samples handles bad n """
# ValueError if n < 1
actual = self.assertRaises(ValueError,
filter_otu_table_to_n_samples,
self.input_otu_table1,
0)
actual = self.assertRaises(ValueError,
filter_otu_table_to_n_samples,
self.input_otu_table1,
-1)
def test_filter_samples_from_distance_matrix(self):
"""filter_samples_from_distance_matrix functions as expected """
actual = filter_samples_from_distance_matrix(parse_distmat(self.input_dm1),
["GHI blah","XYZ"])
self.assertEqual(actual,expected_dm1a)
actual = filter_samples_from_distance_matrix(parse_distmat(self.input_dm1),
["GHI","DEF"])
self.assertEqual(actual,expected_dm1b)
def test_filter_samples_from_distance_matrix_file_input(self):
"""filter_samples_from_distance_matrix handles file input """
actual = filter_samples_from_distance_matrix(self.input_dm1,
["GHI blah","XYZ"])
self.assertEqual(actual,expected_dm1a)
actual = filter_samples_from_distance_matrix(self.input_dm1,
["GHI","DEF"])
self.assertEqual(actual,expected_dm1b)
def test_filter_samples_from_distance_matrix_negate(self):
"""filter_samples_from_distance_matrix functions w negate """
actual = filter_samples_from_distance_matrix(
parse_distmat(self.input_dm1),
["ABC blah","DEF"],
negate=True)
self.assertEqual(actual,expected_dm1a)
actual = filter_samples_from_distance_matrix(\
parse_distmat(self.input_dm1),
["ABC","XYZ"],
negate=True)
self.assertEqual(actual,expected_dm1b)
filter_fasta_expected1 = """>Seq1 some comment
ACCTTGG
>s2 some other comment
TTGG
>S3
AAGGCCGG
"""
filter_fasta_expected2 = """>S5 some comment
CGT
>seq6 some other comment
AA
>S7
T
"""
input_otu_table1 = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
0\t1\t1\t0\t0\tBacteria;Firmicutes
1\t1\t0\t0\t0\tNone
x\t0\t0\t3\t0\tBacteria;Bacteroidetes
z\t0\t1\t0\t1\tNone
""" % __version__
expected_otu_table1a = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
0\t1\t1\t0\t0\tBacteria;Firmicutes
z\t0\t1\t0\t1\tNone""" % __version__
expected_otu_table1b = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
1\t1\t0\t0\t0\tNone
x\t0\t0\t3\t0\tBacteria;Bacteroidetes""" % __version__
input_seqs_to_discard1 = """x
1 some comment
42 not a real otu id"""
expected_otu_table1c = """# QIIME v%s OTU table
#OTU ID\tABC\tXYZ\tConsensus Lineage
0\t1\t0\tBacteria;Firmicutes
1\t1\t0\tNone
z\t0\t1\tNone""" % __version__
expected_otu_table1d = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tConsensus Lineage
0\t1\t1\t0\tBacteria;Firmicutes
1\t1\t0\t0\tNone
x\t0\t0\t3\tBacteria;Bacteroidetes
z\t0\t1\t0\tNone""" % __version__
input_dm1 = """\tABC\tDEF\tGHI\tXYZ
ABC\t0.0\t0.75\t0.00\t0.0063
DEF\t0.75\t0.0\t0.01\t0.65
GHI\t0.00\t0.01\t0.0\t1.0
XYZ\t0.0063\t0.065\t1.0\t0.0"""
expected_dm1a = """\tABC\tDEF
ABC\t0.0\t0.75
DEF\t0.75\t0.0"""
expected_dm1b = """\tABC\tXYZ
ABC\t0.0\t0.0063
XYZ\t0.0063\t0.0"""
input_otu_table2 = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
0\t1\t1\t0\t0\tBacteria;Firmicutes;Something;Something else
1\t1\t0\t0\t0\tNone
0\t1\t1\t0\t2\tBacteria;Firmicutes;Something;Nothing
x\t0\t0\t3\t0\tBacteria;Bacteroidetes
z\t0\t1\t0\t1\tNone;Firmicutes
z\t0\t1\t0\t1\tArchaea""" % __version__
bacteria_otu_table1 = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
0\t1\t1\t0\t0\tBacteria;Firmicutes;Something;Something else
0\t1\t1\t0\t2\tBacteria;Firmicutes;Something;Nothing
x\t0\t0\t3\t0\tBacteria;Bacteroidetes""" % __version__
archaea_otu_table1 = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
z\t0\t1\t0\t1\tArchaea""" % __version__
none_otu_table1 = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
1\t1\t0\t0\t0\tNone
z\t0\t1\t0\t1\tNone;Firmicutes""" % __version__
firmicutes_otu_table1 = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
0\t1\t1\t0\t0\tBacteria;Firmicutes;Something;Something else
0\t1\t1\t0\t2\tBacteria;Firmicutes;Something;Nothing""" % __version__
bacteroidetes_otu_table1 = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
x\t0\t0\t3\t0\tBacteria;Bacteroidetes""" % __version__
nothing_otu_table1 = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
0\t1\t1\t0\t2\tBacteria;Firmicutes;Nothing""" % __version__
none_no_l2_otu_table1 = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
1\t1\t0\t0\t0\tNone""" % __version__
none_firmicutes_otu_table1 = """# QIIME v%s OTU table
#OTU ID\tABC\tDEF\tGHI\tXYZ\tConsensus Lineage
z\t0\t1\t0\t1\tNone;Firmicutes""" % __version__
if __name__ == "__main__":
main()
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