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test_parse.py
executable file
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test_parse.py
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#!/usr/bin/env python
#file test_parse.py
__author__ = "Rob Knight"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Justin Kuczynski", "Greg Caporaso",
"Cathy Lozupone", "Jai Ram Rideout"] #remember to add yourself
__license__ = "BSD"
__version__ = "1.7.0-dev"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Development"
from unittest import TestCase, main
try:
from StringIO import StringIO
except ImportError:
from io import StringIO
from numpy import array
from numpy.testing import assert_almost_equal
from emperor.qiime_backports.parse import (parse_mapping_file,
parse_metadata_state_descriptions, parse_coords, parse_classic_otu_table,
mapping_file_to_dict, parse_mapping_file_to_dict, QiimeParseError)
class TopLevelTests(TestCase):
def setUp(self):
self.otu_table1 = otu_table1
self.otu_table_without_leading_comment = \
otu_table_without_leading_comment
self.otu_table1_floats=otu_table1_floats
self.legacy_otu_table1 = legacy_otu_table1
self.expected_lineages1 = expected_lineages1
def test_parse_mapping_file(self):
"""parse_mapping_file functions as expected"""
s1 = ['#sample\ta\tb', '#comment line to skip',\
'x \t y \t z ', ' ', '#more skip', 'i\tj\tk']
exp = ([['x','y','z'],['i','j','k']],\
['sample','a','b'],\
['comment line to skip','more skip'])
obs = parse_mapping_file(s1)
self.assertEqual(obs, exp)
# We don't currently support this, but we should soon...
# # check that first non-comment, non-blank line is used as
# # header
# s1 = ['sample\ta\tb', '#comment line to skip',\
# 'x \t y \t z ', ' ', '#more skip', 'i\tj\tk']
# exp = ([['x','y','z'],['i','j','k']],\
# ['sample','a','b'],\
# ['comment line to skip','more skip'])
# obs = parse_mapping_file(s1)
# self.assertEqual(obs, exp)
#check that we strip double quotes by default
s2 = ['#sample\ta\tb', '#comment line to skip',\
'"x "\t" y "\t z ', ' ', '"#more skip"', 'i\t"j"\tk']
obs = parse_mapping_file(s2)
self.assertEqual(obs, exp)
def test_mapping_file_to_dict(self):
"""parse_mapping_file functions as expected"""
s1 = ['#sample\ta\tb', '#comment line to skip',\
'x \t y \t z ', ' ', '#more skip', 'i\tj\tk']
exp = ([['x','y','z'],['i','j','k']],\
['sample','a','b'],\
['comment line to skip','more skip'])
mapres = parse_mapping_file(s1) # map_data, header, comments
mapdict = mapping_file_to_dict(*mapres[:2])
expdict = {'x':{'a':'y','b':'z'}, 'i':{'a':'j','b':'k'}}
self.assertEqual(mapdict, expdict)
def test_parse_mapping_file_to_dict(self):
"""parse_mapping_file functions as expected"""
s1 = ['#sample\ta\tb', '#comment line to skip',\
'x \t y \t z ', ' ', '#more skip', 'i\tj\tk']
exp = ([['x','y','z'],['i','j','k']],\
['sample','a','b'],\
['comment line to skip','more skip'])
mapdict, comments = parse_mapping_file_to_dict(s1)
expdict = {'x':{'a':'y','b':'z'}, 'i':{'a':'j','b':'k'}}
self.assertEqual(mapdict, expdict)
self.assertEqual(comments, ['comment line to skip','more skip'])
def test_parse_metadata_state_descriptions(self):
"""parse_metadata_state_descriptions should return correct states from string."""
s = ''
self.assertEqual(parse_metadata_state_descriptions(s), {})
s = 'Study:Twin,Hand,Dog;BodySite:Palm,Stool'
self.assertEqual(parse_metadata_state_descriptions(s), {'Study':set([
'Twin','Hand','Dog']),'BodySite':set(['Palm','Stool'])})
# category names with colons i. e. ontology-derived
s = 'Study:Twin,Hand,Dog;site:UBERON:feces,UBERON:ear canal;'+\
'env_feature:ENVO:farm soil,ENVO:national park'
self.assertEqual(parse_metadata_state_descriptions(s), {'Study':
set(['Twin', 'Hand', 'Dog']), 'site':set(['UBERON:feces',
'UBERON:ear canal']), 'env_feature':set(['ENVO:farm soil',
'ENVO:national park'])})
s = "Treatment:A,B,C;env_matter:ENVO:nitsol,ENVO:farm soil;env_biom:"+\
"ENVO:Tropical dry (including Monsoon forests) and woodlands,"+\
"ENVO:Forest: including woodlands;country:GAZ:Persnickety Islands"+\
",St. Kitt's and Nevis"
self.assertEqual(parse_metadata_state_descriptions(s), {"country":
set(["GAZ:Persnickety Islands", "St. Kitt's and Nevis"]),
"env_biom":set(["ENVO:Tropical dry (including Monsoon forests) "+\
"and woodlands", "ENVO:Forest: including woodlands"]), "env_matter":
set(["ENVO:nitsol","ENVO:farm soil"]), 'Treatment':set(["A", "B",
"C"])})
def test_parse_coords(self):
"""parse_coords should handle coords file"""
coords = """pc vector number\t1\t2\t3
A\t0.11\t0.09\t0.23
B\t0.03\t0.07\t-0.26
C\t0.12\t0.06\t-0.32
eigvals\t4.94\t1.79\t1.50
% variation explained\t14.3\t5.2\t4.3
""".splitlines()
obs = parse_coords(coords)
exp = (['A','B','C'],
array([[.11,.09,.23],[.03,.07,-.26],[.12,.06,-.32]]),
array([4.94,1.79,1.50]),
array([14.3,5.2,4.3]))
# test the header and the values apart from each other
self.assertEqual(obs[0], exp[0])
assert_almost_equal(obs[1], exp[1])
def test_parse_coords_exceptions(self):
"""Check exceptions are raised accordingly with missing information"""
# missing eigenvalues line
with self.assertRaises(QiimeParseError):
out = parse_coords(COORDS_NO_EIGENVALS.splitlines())
# missing percentages explained line
with self.assertRaises(QiimeParseError):
out = parse_coords(COORDS_NO_PCNTS.splitlines())
# missing vector number line
with self.assertRaises(QiimeParseError):
out = parse_coords(COORDS_NO_VECTORS.splitlines())
# a whole different file (taxa summary)
with self.assertRaises(QiimeParseError):
out = parse_coords(taxa_summary1.splitlines())
def test_parse_classic_otu_table_legacy(self):
"""parse_classic_otu_table functions as expected with legacy OTU table
"""
data = self.legacy_otu_table1
data_f = (data.split('\n'))
obs = parse_classic_otu_table(data_f)
exp = (['Fing','Key','NA'],
['0','1','2','3','4'],
array([[19111,44536,42],[1216,3500,6],[1803,1184,2],
[1722,4903,17], [589,2074,34]]),
self.expected_lineages1)
# divide the comparisons into their four elements
self.assertEqual(obs[0], exp[0])
self.assertEqual(obs[1], exp[1])
assert_almost_equal(obs[2], exp[2])
self.assertEqual(obs[3], exp[3])
def test_parse_classic_otu_table(self):
"""parse_classic_otu_table functions as expected with new-style OTU table
"""
data = self.otu_table1
data_f = (data.split('\n'))
obs = parse_classic_otu_table(data_f)
exp = (['Fing','Key','NA'],
['0','1','2','3','4'],
array([[19111,44536,42],[1216,3500,6],[1803,1184,2],
[1722,4903,17], [589,2074,34]]),
self.expected_lineages1)
# divide the comparisons into their four elements
self.assertEqual(obs[0], exp[0])
self.assertEqual(obs[1], exp[1])
assert_almost_equal(obs[2], exp[2])
self.assertEqual(obs[3], exp[3])
# test that the modified parse_classic performs correctly on OTU tables
# without leading comments
data = self.otu_table_without_leading_comment
data_f = (data.split('\n'))
obs = parse_classic_otu_table(data_f)
sams = ['let-7i','miR-7','miR-17n','miR-18a','miR-19a','miR-22',
'miR-25','miR-26a']
otus = ['A2M', 'AAAS', 'AACS', 'AADACL1']
vals = array([\
[-0.2, 0.03680505, 0.205, 0.23, 0.66, 0.08, -0.373, 0.26],
[-0.09, -0.25, 0.274, 0.15, 0.12, 0.29, 0.029, -0.1148452],
[0.33, 0.19, 0.27, 0.28, 0.19, 0.25, 0.089, 0.14],
[0.49, -0.92, -0.723, -0.23, 0.08, 0.49, -0.386, -0.64]])
exp = (sams, otus, vals, []) # no lineages
# because float comps in arrays always errors
self.assertEqual(obs[0], exp[0])
self.assertEqual(obs[1], exp[1])
self.assertEqual(obs[3], exp[3])
self.assertTrue(all((obs[2]==exp[2]).tolist()))
def test_parse_classic_otu_table_floats_in_table(self):
"""parse_classic_otu_table functions using an OTU table containing floats
but cast as int....this will automatically cast into floats"""
data = self.otu_table1_floats
data_f = (data.split('\n'))
obs = parse_classic_otu_table(data_f)
exp = (['Fing','Key','NA'],
['0','1','2','3','4'],
array([[19111.0,44536.0,42.0],[1216.0,3500.0,6.0],
[1803.0,1184.0,2.0],[1722.1,4903.2,17.0],
[589.6,2074.4,34.5]]),
self.expected_lineages1)
# because float comps in arrays always errors
self.assertEqual(obs[0], exp[0])
self.assertEqual(obs[1], exp[1])
self.assertEqual(obs[3], exp[3])
self.assertTrue(all((obs[2]==exp[2]).tolist()))
def test_parse_classic_otu_table_float_counts(self):
"""parse_classic_otu_table should return correct result from small table"""
data = """#Full OTU Counts
#OTU ID Fing Key NA Consensus Lineage
0 19111 44536 42 Bacteria; Actinobacteria; Actinobacteridae; Propionibacterineae; Propionibacterium
1 1216 3500 6 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Lactobacillales; Lactobacillales; Streptococcaceae; Streptococcus
2 1803 1184 2 Bacteria; Actinobacteria; Actinobacteridae; Gordoniaceae; Corynebacteriaceae
3 1722 4903 17 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Staphylococcaceae
4 589 2074 34 Bacteria; Cyanobacteria; Chloroplasts; vectors"""
data_f = (data.split('\n'))
obs = parse_classic_otu_table(data_f,count_map_f=float)
exp = (['Fing','Key','NA'],
['0','1','2','3','4'],
array([[19111.,44536.,42.],[1216.,3500.,6.],[1803.,1184.,2.],\
[1722.,4903.,17.], [589,2074.,34.]]),
[['Bacteria','Actinobacteria','Actinobacteridae','Propionibacterineae','Propionibacterium'],
['Bacteria','Firmicutes','Alicyclobacillaceae','Bacilli','Lactobacillales','Lactobacillales','Streptococcaceae','Streptococcus'],
['Bacteria','Actinobacteria','Actinobacteridae','Gordoniaceae','Corynebacteriaceae'],
['Bacteria','Firmicutes','Alicyclobacillaceae','Bacilli','Staphylococcaceae'],
['Bacteria','Cyanobacteria','Chloroplasts','vectors']])
# because float comps in arrays always errors
self.assertEqual(obs[0], exp[0])
self.assertEqual(obs[1], exp[1])
self.assertEqual(obs[3], exp[3])
self.assertTrue(all((obs[2]==exp[2]).tolist()))
def test_parse_classic_otu_table_file(self):
"""parse_classic_otu_table should return correct result on fileio format object"""
data = """#Full OTU Counts
#OTU ID Fing Key NA Consensus Lineage
0 19111 44536 42 Bacteria; Actinobacteria; Actinobacteridae; Propionibacterineae; Propionibacterium
1 1216 3500 6 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Lactobacillales; Lactobacillales; Streptococcaceae; Streptococcus
2 1803 1184 2 Bacteria; Actinobacteria; Actinobacteridae; Gordoniaceae; Corynebacteriaceae
3 1722 4903 17 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Staphylococcaceae
4 589 2074 34 Bacteria; Cyanobacteria; Chloroplasts; vectors"""
data_f = StringIO(data)
obs = parse_classic_otu_table(data_f)
exp = (['Fing','Key','NA'],
['0','1','2','3','4'],
array([[19111,44536,42],[1216,3500,6],[1803,1184,2],\
[1722,4903,17], [589,2074,34]]),
[['Bacteria','Actinobacteria','Actinobacteridae','Propionibacterineae','Propionibacterium'],
['Bacteria','Firmicutes','Alicyclobacillaceae','Bacilli','Lactobacillales','Lactobacillales','Streptococcaceae','Streptococcus'],
['Bacteria','Actinobacteria','Actinobacteridae','Gordoniaceae','Corynebacteriaceae'],
['Bacteria','Firmicutes','Alicyclobacillaceae','Bacilli','Staphylococcaceae'],
['Bacteria','Cyanobacteria','Chloroplasts','vectors']])
# because float comps in arrays always errors
self.assertEqual(obs[0], exp[0])
self.assertEqual(obs[1], exp[1])
self.assertEqual(obs[3], exp[3])
self.assertTrue(all((obs[2]==exp[2]).tolist()))
def test_parse_classic_otu_table_consensus_lineage(self):
"""parse_classic_otu_table should accept 'consensusLineage'"""
data = """#Full OTU Counts
#OTU ID Fing Key NA consensusLineage
0 19111 44536 42 Bacteria; Actinobacteria; Actinobacteridae; Propionibacterineae; Propionibacterium
1 1216 3500 6 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Lactobacillales; Lactobacillales; Streptococcaceae; Streptococcus
2 1803 1184 2 Bacteria; Actinobacteria; Actinobacteridae; Gordoniaceae; Corynebacteriaceae
3 1722 4903 17 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Staphylococcaceae
4 589 2074 34 Bacteria; Cyanobacteria; Chloroplasts; vectors"""
data_f = StringIO(data)
obs = parse_classic_otu_table(data_f)
exp = (['Fing','Key','NA'],
['0','1','2','3','4'],
array([[19111,44536,42],[1216,3500,6],[1803,1184,2],\
[1722,4903,17], [589,2074,34]]),
[['Bacteria','Actinobacteria','Actinobacteridae','Propionibacterineae','Propionibacterium'],
['Bacteria','Firmicutes','Alicyclobacillaceae','Bacilli','Lactobacillales','Lactobacillales','Streptococcaceae','Streptococcus'],
['Bacteria','Actinobacteria','Actinobacteridae','Gordoniaceae','Corynebacteriaceae'],
['Bacteria','Firmicutes','Alicyclobacillaceae','Bacilli','Staphylococcaceae'],
['Bacteria','Cyanobacteria','Chloroplasts','vectors']])
# because float comps in arrays always errors
self.assertEqual(obs[0], exp[0])
self.assertEqual(obs[1], exp[1])
self.assertEqual(obs[3], exp[3])
self.assertTrue(all((obs[2]==exp[2]).tolist()))
legacy_otu_table1 = """# some comment goes here
#OTU ID Fing Key NA Consensus Lineage
0 19111 44536 42 Bacteria; Actinobacteria; Actinobacteridae; Propionibacterineae; Propionibacterium
1 1216 3500 6 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Lactobacillales; Lactobacillales; Streptococcaceae; Streptococcus
2 1803 1184 2 Bacteria; Actinobacteria; Actinobacteridae; Gordoniaceae; Corynebacteriaceae
3 1722 4903 17 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Staphylococcaceae
4 589 2074 34 Bacteria; Cyanobacteria; Chloroplasts; vectors
"""
otu_table1 = """# Some comment
OTU ID Fing Key NA Consensus Lineage
0 19111 44536 42 Bacteria; Actinobacteria; Actinobacteridae; Propionibacterineae; Propionibacterium
# some other comment
1 1216 3500 6 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Lactobacillales; Lactobacillales; Streptococcaceae; Streptococcus
2 1803 1184 2 Bacteria; Actinobacteria; Actinobacteridae; Gordoniaceae; Corynebacteriaceae
# comments
# everywhere!
3 1722 4903 17 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Staphylococcaceae
4 589 2074 34 Bacteria; Cyanobacteria; Chloroplasts; vectors
"""
otu_table1_floats = """# Some comment
OTU ID Fing Key NA Consensus Lineage
0 19111.0 44536.0 42.0 Bacteria; Actinobacteria; Actinobacteridae; Propionibacterineae; Propionibacterium
# some other comment
1 1216.0 3500.0 6.0 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Lactobacillales; Lactobacillales; Streptococcaceae; Streptococcus
2 1803.0 1184.0 2.0 Bacteria; Actinobacteria; Actinobacteridae; Gordoniaceae; Corynebacteriaceae
# comments
# everywhere!
3 1722.1 4903.2 17 Bacteria; Firmicutes; Alicyclobacillaceae; Bacilli; Staphylococcaceae
4 589.6 2074.4 34.5 Bacteria; Cyanobacteria; Chloroplasts; vectors
"""
otu_table_without_leading_comment = '#OTU ID\tlet-7i\tmiR-7\tmiR-17n\tmiR-18a\tmiR-19a\tmiR-22\tmiR-25\tmiR-26a\nA2M\t-0.2\t0.03680505\t0.205\t0.23\t0.66\t0.08\t-0.373\t0.26\nAAAS\t-0.09\t-0.25\t0.274\t0.15\t0.12\t0.29\t0.029\t-0.114845199\nAACS\t0.33\t0.19\t0.27\t0.28\t0.19\t0.25\t0.089\t0.14\nAADACL1\t0.49\t-0.92\t-0.723\t-0.23\t0.08\t0.49\t-0.386\t-0.64'
expected_lineages1 = [['Bacteria','Actinobacteria','Actinobacteridae','Propionibacterineae','Propionibacterium'],
['Bacteria','Firmicutes','Alicyclobacillaceae','Bacilli','Lactobacillales','Lactobacillales','Streptococcaceae','Streptococcus'],
['Bacteria','Actinobacteria','Actinobacteridae','Gordoniaceae','Corynebacteriaceae'],
['Bacteria','Firmicutes','Alicyclobacillaceae','Bacilli','Staphylococcaceae'],
['Bacteria','Cyanobacteria','Chloroplasts','vectors']]
COORDS_NO_VECTORS = """A\t0.11\t0.09\t0.23
B\t0.03\t0.07\t-0.26
C\t0.12\t0.06\t-0.32
eigvals\t4.94\t1.79\t1.50
% variation explained\t14.3\t5.2\t4.3"""
COORDS_NO_EIGENVALS = """pc vector number\t1\t2\t3
A\t0.11\t0.09\t0.23
B\t0.03\t0.07\t-0.26
C\t0.12\t0.06\t-0.32
foo\t4.94\t1.79\t1.50
% variation explained\t14.3\t5.2\t4.3"""
COORDS_NO_PCNTS = """pc vector number\t1\t2\t3
A\t0.11\t0.09\t0.23
B\t0.03\t0.07\t-0.26
C\t0.12\t0.06\t-0.32
eigvals\t4.94\t1.79\t1.50"""
taxa_summary1 = """#Full OTU Counts
Taxon\tEven1\tEven2\tEven3
Bacteria;Actinobacteria;Actinobacteria(class);Actinobacteridae\t0.0880247251673\t0.0721968465746\t0.081371761759
Bacteria;Bacteroidetes/Chlorobigroup;Bacteroidetes;Bacteroidia\t0.192137761955\t0.191095101593\t0.188504131885
Bacteria;Firmicutes;Bacilli;Lactobacillales\t0.0264895739603\t0.0259942669171\t0.0318460745596
# some comment
Bacteria;Firmicutes;Clostridia;Clostridiales\t0.491800007824\t0.526186212556\t0.49911159984
Bacteria;Firmicutes;Erysipelotrichi;Erysipelotrichales\t0.0311411916592\t0.0184083913576\t0.0282325481054
Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales\t0.166137214246\t0.163087129528\t0.168923372865
No blast hit;Other\t0.00426952518811\t0.00303205147361\t0.0020105109874"""
if __name__ == '__main__':
main()