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test_make_otu_network.py
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test_make_otu_network.py
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#!/usr/bin/env python
# file test_make_otu_network.py
__author__ = "Julia Goodrich"
__copyright__ = "Copyright 2011, The QIIME Project" # consider project name
# remember to add yourself
__credits__ = ["Julia Goodrich", "Jose Carlos Clemente Litran"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "Jose Clemente"
__email__ = "jose.clemente@gmail.com"
from os import remove, close
from os.path import exists
import os
import shutil
from tempfile import mkstemp
from numpy import array
from random import choice, randrange
from tempfile import mkdtemp
from unittest import TestCase, main
from qiime.stats import G_2_by_2
from qiime.make_otu_network import get_sample_info, get_connection_info, \
get_num_con_cat, get_num_cat, make_table_file, make_stats_files,\
make_props_files
from qiime.util import get_qiime_temp_dir, write_biom_table
from biom.table import Table
class OtuNetworkTests(TestCase):
def setUp(self):
self.tmp_dir = get_qiime_temp_dir()
self.map_file = """#SampleID Day time Description
#This is some comment about the study
1 090809 1200 some description of sample1
2 090809 1800 some description of sample2
3 090909 1200 some description of sample3
4 090909 1800 some description of sample4
5 091009 1200 some description of sample5"""
self.cat_by_sample = {"1": [("Day", "090809"), ("time", "1200")],
"2": [("Day", "090809"), ("time", "1800")],
"3": [("Day", "090909"), ("time", "1200")],
"4": [("Day", "090909"), ("time", "1800")],
"5": [("Day", "091009"), ("time", "1200")]}
self.sample_by_cat = {("Day", "090809"): ["1", "2"],
("Day", "090909"): ["3", "4"],
("Day", "091009"): ["5"],
("time", "1200"): ["1", "3", "5"],
("time", "1800"): ["2", "4"]}
self.num_cats = 2
self.meta_dict = {"1": ["090809 1200", 0],
"2": ["090809 1800", 0],
"3": ["090909 1200", 0],
"4": ["090909 1800", 0],
"5": ["091009 1200", 0]}
self.labels = ["from", "to", "eweight", "consensus_lin", "Day", "time"]
self.node_labels = ["node_name", "node_disp_name", "ntype", "degree",
"weighted_degree", "consensus_lin", "Day", "time"]
self.label_list = [["090809", "090909", "091009"], ["1200", "1800"]]
self.otu_table_vals = array([[0, 1, 0, 0, 6],
[2, 0, 0, 0, 0],
[0, 0, 3, 1, 0],
[0, 0, 0, 0, 5],
[0, 4, 2, 0, 0],
[3, 6, 0, 0, 0],
[0, 0, 4, 2, 0],
[0, 0, 0, 0, 3],
[2, 0, 0, 5, 0],
[0, 2, 0, 4, 0]])
otu_table = Table(self.otu_table_vals,
['otu_1', 'otu_2', 'otu_3', 'otu_4', 'otu_5',
'otu_6', 'otu_7', 'otu_8', 'otu_9', 'otu_10'],
['1', '2', '3', '4', '5'],
[{"taxonomy": ["Bacteria", "Actinobacteria",
"Coriobacteridae"]},
{"taxonomy": ["Bacteria", "Bacteroidetes",
"Bacteroidales", "Bacteroidaceae"]},
{"taxonomy": ["Bacteria", "Firmicutes",
"Clostridia", "Clostridiales"]},
{"taxonomy": ["Bacteria", "Spirochaetes",
"Spirochaetales", "Spirochaetaceae"]},
{"taxonomy": ["Bacteria", "Bacteroidetes",
"Bacteroidales", "Rikenellaceae"]},
{"taxonomy": ["Bacteria", "Bacteroidetes",
"Bacteroidales", "Dysgonomonaceae"]},
{"taxonomy": ["Bacteria", "Bacteroidetes",
"Bacteroidales",
"Odoribacteriaceae"]},
{"taxonomy": ["Bacteria", "Bacteroidetes",
"Bacteroidales", "Dysgonomonaceae",
"otu_425"]},
{"taxonomy": ["Bacteria", "Bacteroidetes",
"Bacteroidales", "Dysgonomonaceae",
"otu_425"]},
{"taxonomy": ["Bacteria", "Firmicutes",
"Mollicutes",
"Clostridium_aff_innocuum_CM970"]}],
[None, None, None, None, None])
fd, self.otu_table_fp = mkstemp(
dir=self.tmp_dir, prefix='test_make_otu_network_otu_table',
suffix='.biom')
close(fd)
write_biom_table(otu_table, self.otu_table_fp)
self.otu_sample_file = """#Full OTU Counts
#OTU ID 1 2 3 4 5 Consensus Lineage
otu_1 0 1 0 0 6 Bacteria; Actinobacteria; Coriobacteridae
otu_2 2 0 0 0 0 Bacteria; Bacteroidetes; Bacteroidales; Bacteroidaceae
otu_3 0 0 3 1 0 Bacteria; Firmicutes; Clostridia; Clostridiales
otu_4 0 0 0 0 5 Bacteria; Spirochaetes; Spirochaetales; Spirochaetaceae
otu_5 0 4 2 0 0 Bacteria; Bacteroidetes; Bacteroidales; Rikenellaceae
otu_6 3 6 0 0 0 Bacteria; Bacteroidetes; Bacteroidales; Dysgonomonaceae
otu_7 0 0 4 2 0 Bacteria; Bacteroidetes; Bacteroidales; Odoribacteriaceae
otu_8 0 0 0 0 3 Bacteria; Bacteroidetes; Bacteroidales; Dysgonomonaceae; otu_425
otu_9 2 0 0 5 0 Bacteria; Bacteroidetes; Bacteroidales; Dysgonomonaceae; otu_425
otu_10 0 2 0 4 0 Bacteria; Firmicutes; Mollicutes; Clostridium_aff_innocuum_CM970"""
self.con_by_sample = {
'1': set(['2', '4']), '2': set(['5', '3', '1', '4']),
'3': set(['4', '2']), '4': set(['3', '1', '2']),
'5': set(['2'])}
self.edge_file_str = [
"2 otu_1 1.0 Bacteria:Actinobacteria:Coriobacteridae 090809 1800",
"5 otu_1 6.0 Bacteria:Actinobacteria:Coriobacteridae 091009 1200",
"1 otu_2 2.0 Bacteria:Bacteroidetes:Bacteroidales:Bacteroidaceae 090809 1200",
"3 otu_3 3.0 Bacteria:Firmicutes:Clostridia:Clostridiales 090909 1200",
"4 otu_3 1.0 Bacteria:Firmicutes:Clostridia:Clostridiales 090909 1800",
"5 otu_4 5.0 Bacteria:Spirochaetes:Spirochaetales:Spirochaetaceae 091009 1200",
"2 otu_5 4.0 Bacteria:Bacteroidetes:Bacteroidales:Rikenellaceae 090809 1800",
"3 otu_5 2.0 Bacteria:Bacteroidetes:Bacteroidales:Rikenellaceae 090909 1200",
"1 otu_6 3.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae 090809 1200",
"2 otu_6 6.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae 090809 1800",
"3 otu_7 4.0 Bacteria:Bacteroidetes:Bacteroidales:Odoribacteriaceae 090909 1200",
"4 otu_7 2.0 Bacteria:Bacteroidetes:Bacteroidales:Odoribacteriaceae 090909 1800",
"5 otu_8 3.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae:otu_425 091009 1200",
"1 otu_9 2.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae:otu_425 090809 1200",
"4 otu_9 5.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae:otu_425 090909 1800",
"2 otu_10 2.0 Bacteria:Firmicutes:Mollicutes:Clostridium_aff_innocuum_CM970 090809 1800",
"4 otu_10 4.0 Bacteria:Firmicutes:Mollicutes:Clostridium_aff_innocuum_CM970 090909 1800"]
self.node_file_str = ["1 1 user_node 3 7.0 other 090809 1200",
"2 2 user_node 4 13.0 other 090809 1800",
"3 3 user_node 3 9.0 other 090909 1200",
"4 4 user_node 4 12.0 other 090909 1800",
"5 5 user_node 3 14.0 other 091009 1200",
"otu_1 otu_node 2 7.0 Bacteria:Actinobacteria:Coriobacteridae otu otu",
"otu_2 otu_node 1 2.0 Bacteria:Bacteroidetes:Bacteroidales:Bacteroidaceae otu otu",
"otu_3 otu_node 2 4.0 Bacteria:Firmicutes:Clostridia:Clostridiales otu otu",
"otu_4 otu_node 1 5.0 Bacteria:Spirochaetes:Spirochaetales:Spirochaetaceae otu otu",
"otu_5 otu_node 2 6.0 Bacteria:Bacteroidetes:Bacteroidales:Rikenellaceae otu otu",
"otu_6 otu_node 2 9.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae otu otu",
"otu_7 otu_node 2 6.0 Bacteria:Bacteroidetes:Bacteroidales:Odoribacteriaceae otu otu",
"otu_8 otu_node 1 3.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae:otu_425 otu otu",
"otu_9 otu_node 2 7.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae:otu_425 otu otu",
"otu_10 otu_node 2 6.0 Bacteria:Firmicutes:Mollicutes:Clostridium_aff_innocuum_CM970 otu otu"]
self.red_edge_file_str = [
"2 otu_1 1.0 Bacteria:Actinobacteria:Coriobacteridae 090809 1800",
"5 otu_1 6.0 Bacteria:Actinobacteria:Coriobacteridae 091009 1200",
"1 @1 1.0 missed 090809 1200",
"3 otu_3 3.0 Bacteria:Firmicutes:Clostridia:Clostridiales 090909 1200",
"4 otu_3 1.0 Bacteria:Firmicutes:Clostridia:Clostridiales 090909 1800",
"5 @5 1.0 missed 091009 1200",
"2 otu_5 4.0 Bacteria:Bacteroidetes:Bacteroidales:Rikenellaceae 090809 1800",
"3 otu_5 2.0 Bacteria:Bacteroidetes:Bacteroidales:Rikenellaceae 090909 1200",
"1 otu_6 3.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae 090809 1200",
"2 otu_6 6.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae 090809 1800",
"3 otu_7 4.0 Bacteria:Bacteroidetes:Bacteroidales:Odoribacteriaceae 090909 1200",
"4 otu_7 2.0 Bacteria:Bacteroidetes:Bacteroidales:Odoribacteriaceae 090909 1800",
"1 otu_9 2.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae:otu_425 090809 1200",
"4 otu_9 5.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae:otu_425 090909 1800",
"2 otu_10 2.0 Bacteria:Firmicutes:Mollicutes:Clostridium_aff_innocuum_CM970 090809 1800",
"4 otu_10 4.0 Bacteria:Firmicutes:Mollicutes:Clostridium_aff_innocuum_CM970 090909 1800"]
self.red_node_file_str = ["1 1 user_node 3 7.0 other 090809 1200",
"2 2 user_node 4 13.0 other 090809 1800",
"3 3 user_node 3 9.0 other 090909 1200",
"4 4 user_node 4 12.0 other 090909 1800",
"5 5 user_node 3 14.0 other 091009 1200",
"otu_1 otu_node 2 7.0 Bacteria:Actinobacteria:Coriobacteridae otu otu",
"@1 otu_collapsed 1 1.0 other otu otu",
"otu_3 otu_node 2 4.0 Bacteria:Firmicutes:Clostridia:Clostridiales otu otu",
"@5 otu_collapsed 2 2.0 other otu otu",
"otu_5 otu_node 2 6.0 Bacteria:Bacteroidetes:Bacteroidales:Rikenellaceae otu otu",
"otu_6 otu_node 2 9.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae otu otu",
"otu_7 otu_node 2 6.0 Bacteria:Bacteroidetes:Bacteroidales:Odoribacteriaceae otu otu",
"otu_9 otu_node 2 7.0 Bacteria:Bacteroidetes:Bacteroidales:Dysgonomonaceae:otu_425 otu otu",
"otu_10 otu_node 2 6.0 Bacteria:Firmicutes:Mollicutes:Clostridium_aff_innocuum_CM970 otu otu"]
self.otu_dc = {1: 3, 2: 7}
self.sample_dc = {3: 3, 4: 2}
self.degree_counts = {1: 3, 2: 7, 3: 3, 4: 2}
self.num_con_cat = {"Day": 2,
"time": 1}
self.num_con = 6
self.num_cat = {"Day": 2,
"time": 4}
self.num_cat_less = {"Day": 1,
"time": 3}
self._paths_to_clean_up = [self.otu_table_fp]
self._dir_to_clean_up = ''
def tearDown(self):
map(remove, self._paths_to_clean_up)
if self._dir_to_clean_up != '':
shutil.rmtree(self._dir_to_clean_up)
def test_get_sample_info(self):
cat_by_sample, sample_by_cat, num_cats, meta_dict, labels, node_labels, \
label_list = get_sample_info(self.map_file.split('\n'))
self.assertEqual(cat_by_sample, self.cat_by_sample)
self.assertEqual(sample_by_cat, self.sample_by_cat)
self.assertEqual(num_cats, self.num_cats)
self.assertEqual(meta_dict, self.meta_dict)
self.assertEqual(labels, self.labels)
self.assertEqual(node_labels, self.node_labels)
self.assertEqual(label_list, self.label_list)
def test_get_connection_info(self):
con_by_sample, node_file_str, edge_file_str, red_node_file_str,\
red_edge_file_str, otu_dc, degree_counts, sample_dc = \
get_connection_info(self.otu_table_fp, self.num_cats,
self.meta_dict)
# get_connection_info(self.otu_sample_file.split('\n'), self.num_cats,\
# self.meta_dict)
self.assertEqual(con_by_sample, self.con_by_sample)
self.assertEqual(set(node_file_str), set(self.node_file_str))
self.assertEqual(set(edge_file_str), set(self.edge_file_str))
self.assertEqual(set(red_node_file_str), set(self.red_node_file_str))
self.assertEqual(set(red_edge_file_str), set(self.red_edge_file_str))
self.assertEqual(otu_dc, self.otu_dc)
self.assertEqual(degree_counts, self.degree_counts)
self.assertEqual(sample_dc, self.sample_dc)
def test_get_num_con_cat(self):
num_con_cat, num_con = get_num_con_cat(
self.con_by_sample, self.cat_by_sample)
self.assertEqual(num_con_cat, self.num_con_cat)
self.assertEqual(num_con, self.num_con)
def test_get_num_cat(self):
num_cat = get_num_cat(self.sample_by_cat, self.cat_by_sample.keys())
self.assertEqual(num_cat, self.num_cat)
num_cat = get_num_cat(
self.sample_by_cat,
self.cat_by_sample.keys()[:-1])
self.assertEqual(num_cat, self.num_cat_less)
def test_make_table_file(self):
random_dir_name = mkdtemp()
foldername = random_dir_name
self._dir_to_clean_up = foldername
try:
os.mkdir(foldername)
except OSError:
pass
obs = foldername
try:
os.mkdir(os.path.join(obs, "otu_network"))
except OSError:
pass
obs = os.path.join(obs, "otu_network")
make_table_file(
self.edge_file_str,
self.labels,
obs,
"real_edge_table.txt")
self.assertTrue(exists(foldername + "/otu_network/real_edge_table.txt"), 'The file was not created in \
the appropriate location')
def test_make_stats_files(self):
random_dir_name = mkdtemp()
foldername = random_dir_name
self._dir_to_clean_up = foldername
try:
os.mkdir(foldername)
except OSError:
pass
obs = foldername
try:
os.mkdir(os.path.join(obs, "otu_network"))
except OSError:
pass
try:
os.mkdir(os.path.join(obs, "otu_network/stats"))
except OSError:
pass
obs = os.path.join(obs, "otu_network")
make_stats_files(
self.sample_dc,
self.otu_dc,
self.degree_counts,
self.num_con_cat,
self.num_con,
self.num_cat,
self.cat_by_sample,
obs)
self.assertTrue(exists(foldername + "/otu_network/stats/real_dc_otu_degree.txt"), 'The file was not created in \
the appropriate location')
self.assertTrue(exists(foldername + "/otu_network/stats/real_dc_sample_degree.txt"), 'The file was not created in \
the appropriate location')
self.assertTrue(exists(foldername + "/otu_network/stats/real_dc_sample_otu_degree.txt"), 'The file was not created in \
the appropriate location')
self.assertTrue(exists(foldername + "/otu_network/stats/real_cat_stats_Day.txt"), 'The file was not created in \
the appropriate location')
self.assertTrue(exists(foldername + "/otu_network/stats/real_cat_stats_time.txt"), 'The file was not created in \
the appropriate location')
def test_make_props_files(self):
random_dir_name = mkdtemp()
foldername = random_dir_name
self._dir_to_clean_up = foldername
try:
os.mkdir(foldername)
except OSError:
pass
obs = foldername
try:
os.mkdir(os.path.join(obs, "otu_network"))
except OSError:
pass
try:
os.mkdir(os.path.join(obs, "otu_network/props"))
except OSError:
pass
obs = os.path.join(obs, "otu_network")
self.assertTrue(exists(foldername + "/otu_network/props/"), 'The file was not created in \
the appropriate location')
self.assertTrue(exists(foldername + "/otu_network/props"), 'The file was not created in \
the appropriate location')
if __name__ == '__main__':
main()