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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 2010, The QIIME Project" #consider project name
__credits__ = ["Julia Goodrich"] #remember to add yourself
__license__ = "GPL"
__version__ = "1.2.1"
__maintainer__ = "Jose Clemente"
__email__ = "jose.clemente@gmail.com"
__status__ = "Release"
from cogent.util.unit_test import TestCase, main
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 cogent.util.misc import get_random_directory_name
from cogent.maths.stats.test import G_2_by_2
from random import choice, randrange
from os import remove
from os.path import exists
import os
import shutil
class OtuNetworkTests(TestCase):
def setUp(self):
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_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._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_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=get_random_directory_name(output_dir='/tmp')
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=get_random_directory_name(output_dir='/tmp')
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=get_random_directory_name(output_dir='/tmp')
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()