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#!/usr/bin/env python
# File created on 17 Aug 2010
from __future__ import division
__author__ = "Jens Reeder"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder","Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Justin Kuczynski"
__email__ = "justinak@gmail.com"
__status__ = "Release"
from os.path import exists,abspath
from shutil import rmtree
from numpy import array
from matplotlib.axes import Subplot
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import remove_files
from qiime.util import get_tmp_filename
from qiime.plot_rank_abundance_graph import make_sorted_frequencies,\
plot_rank_abundance_graph, plot_rank_abundance_graphs
from qiime.util import create_dir
class PlotRankAbundance(TestCase):
def setUp(self):
self.tmp_dir='/tmp/'
self.files_to_remove = []
self._dirs_to_remove=[]
def tearDown(self):
remove_files(self.files_to_remove)
if self._dirs_to_remove:
for i in self._dirs_to_remove:
rmtree(i)
def test_make_sorted_frequencies(self):
"""make_sorted_frequencies transforms and sorts correctly"""
#works on empty
counts = array([])
self.assertEqual(make_sorted_frequencies(counts),[])
#works on zeros
counts = array([0,0,0,0,0,0])
self.assertEqual(make_sorted_frequencies(counts),[])
#works on flat data
counts = array([3,3,3,3,3])
expected_freqs = [0.2, 0.2, 0.2, 0.2, 0.2]
observed_freqs = make_sorted_frequencies(counts)
self.assertEqual(observed_freqs, expected_freqs)
#works on real data
counts = array([1,2,0,1,0,2,4])
expected_freqs = [0.4, 0.2, 0.2, 0.1, 0.1]
observed_freqs = make_sorted_frequencies(counts)
self.assertEqual(observed_freqs, expected_freqs)
def test_make_sorted_frequencies_abolute(self):
"""make_sorted_frequencies returns correct absolute values"""
#works on empty
counts = array([])
self.assertEqual(make_sorted_frequencies(counts,True),[])
#works on zeros
counts = array([0,0,0,0,0,0])
self.assertEqual(make_sorted_frequencies(counts,True),[])
#works on flat data
counts = array([3,3,3,3,3])
expected_freqs = [3,3,3,3,3]
observed_freqs = make_sorted_frequencies(counts,True)
self.assertEqual(observed_freqs, expected_freqs)
#works o real data
counts = array([1,2,0,1,0,2,4])
expected_freqs = [4,2,2,1,1]
observed_freqs = make_sorted_frequencies(counts,True)
self.assertEqual(observed_freqs, expected_freqs)
def test_plot_rank_abundance_graph(self):
"""plot_rank_abudance_graph plots something"""
counts = array([20,15,12,8,4,2,1,3,1,2])
observed = plot_rank_abundance_graph(counts)
# can we test something more clever here?
# basically just tests that something is drawn, but not what
self.assertEqual(type(observed), Subplot)
def test_plot_rank_abundance_graphs_filetype(self):
"""plot_rank_abundance_graphs works with all filetypes"""
self.otu_table = otu_table_fake.split('\n')
self.dir = get_tmp_filename(tmp_dir=self.tmp_dir,
prefix="test_plot_rank_abundance",
suffix="/")
create_dir(self.dir)
self._dirs_to_remove.append(self.dir)
#test all supported filetypes
for file_type in ['pdf','svg','png','eps']:
plot_rank_abundance_graphs('S3', iter(self.otu_table), self.dir,
file_type=file_type)
tmp_file = abspath(self.dir+"rank_abundance_cols_0."+file_type)
self.files_to_remove.append(tmp_file)
self.assertTrue(exists(tmp_file))
def test_plot_rank_abundance_graphs(self):
"""plot_rank_abundance_graphs works with any number of samples"""
self.otu_table = otu_table_fake.split('\n')
self.dir = get_tmp_filename(tmp_dir=self.tmp_dir,
prefix="test_plot_rank_abundance",
suffix="/")
create_dir(self.dir)
self._dirs_to_remove.append(self.dir)
#test empty sample name
self.assertRaises(ValueError, plot_rank_abundance_graphs, '',
iter(self.otu_table), self.dir)
#test invalid sample name
self.assertRaises(ValueError, plot_rank_abundance_graphs,
'Invalid_sample_name',
iter(self.otu_table), self.dir)
#test with two samples
file_type="pdf"
plot_rank_abundance_graphs('S3,S5', iter(self.otu_table), self.dir,
file_type=file_type)
tmp_file = abspath(self.dir+"rank_abundance_cols_0_2."+file_type)
self.assertTrue(exists(tmp_file))
self.files_to_remove.append(tmp_file)
# test with all samples
plot_rank_abundance_graphs('*', iter(self.otu_table), self.dir,
file_type=file_type)
tmp_file = abspath(self.dir+"rank_abundance_cols_0_1_2."+file_type)
self.files_to_remove.append(tmp_file)
self.assertTrue(exists(tmp_file))
otu_table_fake = """#Full OTU Counts
#OTU ID S3 S4 S5 Consensus Lineage
0 1 0 1 Root;Bacteria
3 2 0 1 Root;Bacteria;Acidobacteria
4 1 0 9 Root;Bacteria;Bacteroidetes
2 1 0 1 Root;Bacteria;Acidobacteria;Acidobacteria;Gp5
6 1 25 42 Root;Archaea"""
if __name__ == "__main__":
main()
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