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test_simsam.py
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test_simsam.py
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#!/usr/bin/env python
# File created on 19 Mar 2011
from __future__ import division
__author__ = "Justin Kucyznski"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kucyznski"]
__license__ = "GPL"
__version__ = "1.6.0"
__maintainer__ = "Justin Kucyznski"
__email__ = "justinak@gmail.com"
__status__ = "Release"
from cogent.util.unit_test import TestCase, main
from cogent.parse.tree import DndParser
from biom.parse import parse_biom_table
from qiime.util import get_qiime_scripts_dir, load_qiime_config
from biom.table import table_factory
import tempfile
import string
import random
import os
import shutil
import subprocess
import numpy
import qiime.simsam
class SimsamTests(TestCase):
def setUp(self):
self.dirs_to_remove = []
def tearDown(self):
for d in self.dirs_to_remove:
if os.path.exists(d):
shutil.rmtree(d)
def test_script(self):
""" test the whole simsam script
"""
qiime_config = load_qiime_config()
tempdir = qiime_config['temp_dir'] or tempfile.gettempdir()
maindir = os.path.join(tempdir,
''.join(random.choice(string.ascii_letters + string.digits) \
for x in range(10)))
os.makedirs(maindir)
self.dirs_to_remove.append(maindir)
otuf = os.path.join(maindir,'otuf')
treef = os.path.join(maindir,'treef')
otufh = open(otuf,'w')
otufh.write(tutorial_otu_table)
otufh.close()
treefh = open(treef,'w')
treefh.write(tutorial_tree)
treefh.close()
scripts_dir = get_qiime_scripts_dir()
cmd = scripts_dir+'/simsam.py -i %s -t %s -o %s -d .003 -n 3 ' %\
(otuf, treef, maindir+'/simsam_out.txt')
proc = subprocess.Popen(cmd,shell=True,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
scriptout, scripterr = proc.communicate()
if scriptout:
raise RuntimeError('script returned stdout: ' + scriptout)
if scripterr:
raise RuntimeError('script returned stderr: ' + scripterr)
num_replicates = 3 # ensure this matches cmd above
res = open(maindir+'/simsam_out.txt','U')
orig_table = parse_biom_table(open(otuf,'U'))
res_table = parse_biom_table(res)
# 3 samples per input sample
self.assertEqual(len(res_table.SampleIds),num_replicates*len(orig_table.SampleIds))
# sample_ids have correct naming and order
for i in range(len(orig_table.SampleIds)):
for j in range(num_replicates):
exp = orig_table.SampleIds[i] +'.'+str(j)
self.assertEqual(res_table.SampleIds[i*num_replicates+j],exp)
# same total sequences in each replicate sample
num_orig_samples = len(orig_table.SampleIds)
orig_sams = orig_table.iterSampleData()
res_sams = res_table.iterSampleData()
for i in range(num_orig_samples):
orig_sam = orig_sams.next()
for j in range(num_replicates):
res_sam = res_sams.next()
self.assertEqual(res_sam.sum(), orig_sam.sum())
# would be nice to test that result otu table doesn't match input,
# but not sure how probable that is, and don't want stochastic failures
def test_script_nochange(self):
""" simsam script with 0 distance should just replicate input samples
"""
qiime_config = load_qiime_config()
tempdir = qiime_config['temp_dir'] or tempfile.gettempdir()
maindir = os.path.join(tempdir,
''.join(random.choice(string.ascii_letters + string.digits) \
for x in range(10)))
os.makedirs(maindir)
self.dirs_to_remove.append(maindir)
otuf = os.path.join(maindir,'otuf')
treef = os.path.join(maindir,'treef')
otufh = open(otuf,'w')
otufh.write(tutorial_otu_table)
otufh.close()
treefh = open(treef,'w')
treefh.write(tutorial_tree)
treefh.close()
scripts_dir = get_qiime_scripts_dir()
cmd = scripts_dir+'/simsam.py -i %s -t %s -o %s -d 0 -n 3 ' %\
(otuf, treef, maindir+'/simsam_out.txt')
proc = subprocess.Popen(cmd,shell=True,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
scriptout, scripterr = proc.communicate()
if scriptout:
raise RuntimeError('script returned stdout: ' + scriptout)
if scripterr:
raise RuntimeError('script returned stderr: ' + scripterr)
num_replicates = 3 # ensure this matches cmd above
res = open(maindir+'/simsam_out.txt','U')
orig_table = parse_biom_table(open(otuf,'U'))
res_table = parse_biom_table(res)
# 3 samples per input sample
self.assertEqual(len(res_table.SampleIds),num_replicates*len(orig_table.SampleIds))
# sample_ids have correct naming and order
for i in range(len(orig_table.SampleIds)):
for j in range(num_replicates):
exp = orig_table.SampleIds[i] +'.'+str(j)
self.assertEqual(res_table.SampleIds[i*num_replicates+j],exp)
# same otu ids
self.assertEqual(res_table.ObservationIds, orig_table.ObservationIds)
# same otu table, just replicated thrice
# note this requires the same sorting of otus, input is correct sorting
num_orig_samples = len(orig_table.SampleIds)
orig_sams = orig_table.iterSampleData()
res_sams = res_table.iterSampleData()
for i in range(num_orig_samples):
orig_sam = orig_sams.next()
for j in range(num_replicates):
res_sam = res_sams.next()
self.assertEqual(res_sam, orig_sam)
def test_sim_otu_table(self):
""" simulated otu table should be right order, number of seqs
tree looks like:
/-A
|
---------|--B
|
| /-C
\--------|
\-D
"""
sample_ids = ['samB','samA']
otu_ids = ['C','A']
otu_mtx = numpy.array([ [3,9],
[5,0],
])
otu_metadata = [{'tax':'otu_C is cool'},{'tax':''}]
tree = DndParser("(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);")
num_replicates = 3
dissimilarity = 0.15
rich_table = table_factory(otu_mtx,sample_ids,otu_ids,
observation_metadata=otu_metadata)
res_sam_names, res_otus, res_otu_mtx, res_otu_metadata = \
qiime.simsam.sim_otu_table(sample_ids, otu_ids, rich_table.iterSamples(), otu_metadata,
tree, num_replicates, dissimilarity)
# dissim is too small to change otu C, it should always be there
# with at least original # seqs, maybe more
c_index = res_otus.index('C')
c_row = res_otu_mtx[c_index]
self.assertEqual(res_otu_metadata[c_index],{'tax':'otu_C is cool'})
self.assertGreaterThan(c_row,[2,2,2,8,8,8])
# order of samples should remain the same as input,
# and eash replicate sample
# should have same number or sequences as input
for i in range(len(sample_ids)):
for j in range(num_replicates):
self.assertEqual(otu_mtx[:,i].sum(),
res_otu_mtx[:,num_replicates*i+j].sum())
def test_get_new_otu_id_small(self):
""" small dissim should return old tip id"""
tree = DndParser("(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);")
res = qiime.simsam.get_new_otu_id(old_otu_id='A', tree=tree, dissim=.05)
self.assertEqual(res,'A')
def test_get_new_otu_id_large(self):
""" w/ large dissim, should at least sometimes return other tip"""
tree = DndParser("(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);")
results = []
for i in range(1000):
results.append(qiime.simsam.get_new_otu_id(old_otu_id='D',
tree=tree, dissim=.6))
self.assertContains(results,'C')
self.assertContains(results,'D')
self.assertNotContains(results,'A')
self.assertNotContains(results,'B')
def test_combine_sample_dicts(self):
""" combining sample dicts should give correct otu table and sorting
"""
d1 = {'otu2':0,'otu1':3}
d2 = {'otu4':5}
d3 = {}
res_otu_mtx, res_otu_ids = qiime.simsam.combine_sample_dicts([d1,d2,d3])
exp_otu_ids = ['otu1','otu2','otu4']
exp_otu_mtx = numpy.array([ [3,0,0],
[0,0,0],
[0,5,0],
])
self.assertEqual(res_otu_ids, exp_otu_ids)
self.assertEqual(res_otu_mtx, exp_otu_mtx)
tutorial_tree = 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tutorial_otu_table = """{"rows": [{"id": "0", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae"]}}, {"id": "1", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Bacteroidetes", "c__Bacteroidia", "o__Bacteroidales", "f__"]}}, {"id": "2", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Staphylococcaceae"]}}, {"id": "3", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "4", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "5", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", "f__Lachnospiraceae"]}}, {"id": "6", "metadata": {"taxonomy": ["Root", "k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Clostridiales", 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[375, 2, 2.0], [376, 4, 1.0], [377, 5, 5.0], [377, 6, 9.0], [377, 7, 5.0], [377, 8, 3.0], [378, 0, 2.0], [378, 1, 18.0], [378, 3, 1.0], [378, 6, 21.0], [378, 7, 4.0], [378, 8, 4.0], [379, 3, 1.0], [380, 1, 2.0], [380, 5, 1.0], [381, 2, 1.0], [382, 0, 1.0], [382, 2, 1.0], [383, 2, 1.0], [384, 2, 1.0], [384, 7, 1.0], [385, 2, 1.0], [385, 8, 1.0], [386, 6, 1.0], [387, 1, 19.0], [387, 2, 2.0], [387, 4, 2.0], [387, 6, 3.0], [388, 7, 1.0], [389, 2, 1.0], [390, 2, 1.0], [391, 3, 1.0], [392, 2, 1.0], [393, 0, 1.0], [393, 1, 1.0], [393, 2, 1.0], [394, 1, 1.0], [394, 2, 2.0], [394, 4, 9.0], [394, 5, 1.0], [394, 6, 1.0], [394, 7, 1.0], [394, 8, 3.0], [395, 6, 2.0], [396, 1, 2.0], [396, 2, 3.0], [396, 3, 1.0], [396, 4, 4.0], [396, 6, 5.0], [396, 8, 4.0], [397, 6, 1.0], [398, 8, 1.0], [399, 1, 2.0], [399, 2, 1.0], [399, 3, 2.0], [399, 6, 1.0], [399, 7, 1.0], [399, 8, 1.0], [400, 1, 1.0], [401, 3, 1.0], [402, 1, 1.0], [403, 6, 1.0], [404, 6, 4.0], [405, 1, 1.0], [405, 6, 3.0], [406, 8, 1.0], [407, 3, 9.0], [407, 6, 3.0], [408, 4, 1.0], [409, 8, 1.0], [410, 0, 1.0], [411, 2, 1.0], [412, 6, 8.0], [412, 7, 10.0], [412, 8, 2.0], [413, 2, 1.0], [413, 3, 3.0], [414, 1, 1.0], [415, 3, 1.0], [416, 3, 1.0]], "columns": [{"id": "PC.354", "metadata": null}, {"id": "PC.355", "metadata": null}, {"id": "PC.356", "metadata": null}, {"id": "PC.481", "metadata": null}, {"id": "PC.593", "metadata": null}, {"id": "PC.607", "metadata": null}, {"id": "PC.634", "metadata": null}, {"id": "PC.635", "metadata": null}, {"id": "PC.636", "metadata": null}], "generated_by": "QIIME 1.4.0-dev, svn revision 2520", "matrix_type": "sparse", "shape": [417, 9], "format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html", "date": "2011-12-20T17:28:05.299943", "type": "OTU table", "id": null, "matrix_element_type": "float"}"""
if __name__ == "__main__":
main()