#!/usr/bin/env python
#file test_make_otu_heatmap_html.py
__author__ = "Jesse Stombaugh"
__copyright__ = "Copyright 2011, The QIIME Project" #consider project name
__credits__ = ["Jesse Stombaugh"] #remember to add yourself
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
__status__ = "Release"
from numpy import array, log
from cogent.util.unit_test import TestCase, main
from qiime.make_otu_heatmap_html import (make_html_doc,create_javascript_array,\
filter_by_otu_hits,line_converter,\
get_log_transform)
class TopLevelTests(TestCase):
"""Tests of top-level functions"""
def setUp(self):
"""define some top-level data"""
self.col_header=['Sample1', 'Sample2']
self.row_header=['OTU1','OTU2']
self.otu_table=array([[0,0],[1,5]])
self.lineages=[['Bacteria'],['Archaea']]
self.data={}
self.data['otu_counts']=self.col_header,self.row_header,self.otu_table,\
self.lineages
self.num_otu_hits=5
def test_make_html_doc(self):
"""make_html_doc: create the web interface for otu heatmaps"""
obs = make_html_doc('./test/test_otu_count_table.js')
self.assertEqual(obs,exp_html_script)
def test_create_javascript_array(self):
"""create_javascript_array: takes a numpy array and generates a
javascript array"""
self.rows=[['#OTU ID', 'OTU2'],['Sample1',1],['Sample2',5],\
['Consensus Lineage','Archaea']]
obs=create_javascript_array(self.rows)
self.assertEqual(obs,exp_js_array)
def test_filter_by_otu_hits(self):
"""filter_by_otu_hits: filters the table by otu hits per otu"""
exp=array([['#OTU ID', 'OTU2'],['Sample1',1],['Sample2',5],\
['Consensus Lineage','Archaea;']])
obs=filter_by_otu_hits(self.num_otu_hits,self.data)
self.assertEqual(obs,exp)
def test_get_log_transform(self):
data = array([[0,1,2],[1000,0,0]])
logdata = get_log_transform(data,eps=None)
# set zeros to 1/2s
exp = log(array([[.5,1,2],[1000,.5,.5]]))
# translate to 0
exp -= exp.min()
self.assertFloatEqual(logdata, exp)
exp_js_array='''\
var OTU_table=new Array();\n\
var i=0;\n\
for (i==0;i<4;i++) {\n\
OTU_table[i]=new Array();}\n\
OTU_table[0][0]='#OTU ID';\n\
OTU_table[0][1]='OTU2';\n\
OTU_table[1][0]='Sample1';\n\
OTU_table[1][1]=1;\n\
OTU_table[2][0]='Sample2';\n\
OTU_table[2][1]=5;\n\
OTU_table[3][0]='Consensus Lineage';\n\
OTU_table[3][1]='Archaea';\n\
'''
exp_html_script = \
r'''
Filter by Counts per OTU:
'''
#run tests if called from command line
if __name__ == "__main__":
main()