def test_get_log_transform(self):
orig_data = array([[0, 1, 2], [1000, 0, 0]])
orig_otu_table = table_factory(orig_data,
['Sample1', 'Sample2', 'Sample3'],
['OTU1', 'OTU2'], [None, None, None], [{
"taxonomy": ["Bacteria"]
}, {
"taxonomy": ["Archaea"]
}])
exp_data = array([[0, 0.69314718, 1.38629436], [7.60090246, 0, 0]])
exp_otu_table = table_factory(exp_data,
['Sample1', 'Sample2', 'Sample3'],
['OTU1', 'OTU2'], [None, None, None], [{
"taxonomy": ["Bacteria"]
}, {
"taxonomy": ["Archaea"]
}])
log_otu_table = get_log_transform(orig_otu_table, eps=None)
# comparing directly log_otu_table against exp_otu_table doesn't work,
# needs to be modified in the otu table object
self.assertFloatEqual(list(log_otu_table.iterSampleData()),
list(exp_otu_table.iterSampleData()))
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)
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)
orig_data = array([[0, 1, 2], [1000, 0, 0]])
#{(0,1):1.0, (0,2):2,(1,0):1000.0}
orig_otu_table = table_factory(orig_data,
['Sample1', 'Sample2', 'Sample3'],
['OTU1', 'OTU2'], [None, None, None], [{
"taxonomy": ["Bacteria"]
}, {
"taxonomy": ["Archaea"]
}])
exp_data = array([[0, 0.69314718, 1.38629436], [7.60090246, 0, 0]])
#{(0,1):0.69314718, (0,2):1.38629436,(1,0):7.60090246}
exp_otu_table = table_factory(exp_data,
['Sample1', 'Sample2', 'Sample3'],
['OTU1', 'OTU2'], [None, None, None], [{
"taxonomy": ["Bacteria"]
}, {
"taxonomy": ["Archaea"]
}])
log_otu_table = get_log_transform(orig_otu_table, eps=None)
# comparing directly log_otu_table against exp_otu_table doesn't work,
# needs to be modified in the otu table object
self.assertFloatEqual(log_otu_table._data.items(),
exp_otu_table._data.items())
def test_get_log_transform(self):
orig_data = array([[0, 1, 2], [1000, 0, 0]])
orig_otu_table = table_factory(orig_data,
['Sample1', 'Sample2', 'Sample3'],
['OTU1', 'OTU2'],
[None, None, None],
[{"taxonomy": ["Bacteria"]},
{"taxonomy": ["Archaea"]}])
exp_data = array([[0, 0.69314718, 1.38629436], [7.60090246, 0, 0]])
exp_otu_table = table_factory(exp_data,
['Sample1', 'Sample2', 'Sample3'],
['OTU1', 'OTU2'],
[None, None, None],
[{"taxonomy": ["Bacteria"]},
{"taxonomy": ["Archaea"]}])
log_otu_table = get_log_transform(orig_otu_table, eps=None)
# comparing directly log_otu_table against exp_otu_table doesn't work,
# needs to be modified in the otu table object
assert_almost_equal(list(log_otu_table.iterSampleData()),
list(exp_otu_table.iterSampleData()))
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)
orig_data = array([[0,1,2],[1000,0,0]])
#{(0,1):1.0, (0,2):2,(1,0):1000.0}
orig_otu_table = table_factory(orig_data,
['Sample1', 'Sample2', 'Sample3'],
['OTU1', 'OTU2'],
[None, None, None],
[{"taxonomy": ["Bacteria"]},
{"taxonomy": ["Archaea"]}])
exp_data = array([[0,0.69314718,1.38629436],[7.60090246,0,0]])
#{(0,1):0.69314718, (0,2):1.38629436,(1,0):7.60090246}
exp_otu_table = table_factory(exp_data,
['Sample1', 'Sample2', 'Sample3'],
['OTU1', 'OTU2'],
[None, None, None],
[{"taxonomy": ["Bacteria"]},
{"taxonomy": ["Archaea"]}])
log_otu_table = get_log_transform(orig_otu_table, eps = None)
# comparing directly log_otu_table against exp_otu_table doesn't work,
# needs to be modified in the otu table object
self.assertFloatEqual(list(log_otu_table.iterSampleData()),
list(exp_otu_table.iterSampleData()))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
data = {}
#Open and get coord data
#data['otu_counts'] = list(get_otu_counts(opts.otu_table_fp, data))
otu_table = get_otu_counts(opts.otu_table_fp)
# determine whether fractional values are present in OTU table
num_otu_hits = opts.num_otu_hits
if opts.log_transform:
if not opts.log_eps is None and opts.log_eps <= 0:
print "Parameter 'log_eps' must be positive. Value was", opts.log_eps
exit(1)
#data['otu_counts'][2] = get_log_transform(data['otu_counts'][2], opts.log_eps)
otu_table = get_log_transform(otu_table, opts.log_eps)
num_otu_hits = 0
fractional_values = False
max_val = -1
for val in otu_table.iterObservationData():
max_val = maximum(max_val, val.max())
# the data cannot be of mixed types: if one is float, all are float
fractional_values = (max_val.dtype.name == 'float32'
or max_val.dtype.name == 'float64')
if fractional_values and max_val <= 1:
if num_otu_hits > 0:
print "Warning: OTU table appears to be using relative abundances",\
"and num_otu_hits was set to %d. Setting num_otu_hits to 0."\
%(num_otu_hits)
num_otu_hits = 0
filepath = opts.otu_table_fp
filename = filepath.strip().split('/')[-1].split('.')[0]
dir_path = opts.output_dir
create_dir(dir_path)
js_dir_path = os.path.join(dir_path, 'js')
create_dir(js_dir_path)
qiime_dir = get_qiime_project_dir()
js_path = os.path.join(qiime_dir, 'qiime/support_files/js')
shutil.copyfile(os.path.join(js_path, 'overlib.js'),
os.path.join(js_dir_path, 'overlib.js'))
shutil.copyfile(os.path.join(js_path, 'otu_count_display.js'),
os.path.join(js_dir_path, 'otu_count_display.js'))
shutil.copyfile(os.path.join(js_path, 'jquery.js'),
os.path.join(js_dir_path, 'jquery.js'))
shutil.copyfile(os.path.join(js_path, 'jquery.tablednd_0_5.js'),
os.path.join(js_dir_path, 'jquery.tablednd_0_5.js'))
# load tree for sorting OTUs
ordered_otu_names = None
if not opts.tree is None:
try:
f = open(opts.tree, 'U')
except (TypeError, IOError):
raise TreeMissingError, \
"Couldn't read tree file at path: %s" % tree_source
tree = parse_newick(f, PhyloNode)
f.close()
ordered_otu_names = [tip.Name for tip in tree.iterTips()]
ordered_sample_names = None
# load tree for sorting Samples
if not opts.sample_tree is None:
try:
f = open(opts.sample_tree, 'U')
except (TypeError, IOError):
raise TreeMissingError, \
"Couldn't read tree file at path: %s" % tree_source
tree = parse_newick(f, PhyloNode)
f.close()
ordered_sample_names = [tip.Name for tip in tree.iterTips()]
# if there's no sample tree, load sample map for sorting samples
elif not opts.map_fname is None:
lines = open(opts.map_fname, 'U').readlines()
map = parse_mapping_file(lines)[0]
ordered_sample_names = [row[0] for row in map]
#data['otu_order'] = ordered_otu_names
#data['sample_order'] = ordered_sample_names
try:
action = generate_heatmap_plots
except NameError:
action = None
#Place this outside try/except so we don't mask NameError in action
if action:
action(num_otu_hits, otu_table, ordered_otu_names,
ordered_sample_names, dir_path, js_dir_path, filename,
fractional_values)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
data = {}
#Open and get coord data
#data['otu_counts'] = list(get_otu_counts(opts.otu_table_fp, data))
otu_table = get_otu_counts(opts.otu_table_fp)
# determine whether fractional values are present in OTU table
num_otu_hits=opts.num_otu_hits
if opts.log_transform:
if not opts.log_eps is None and opts.log_eps <= 0:
print "Parameter 'log_eps' must be positive. Value was", opts.log_eps
exit(1)
#data['otu_counts'][2] = get_log_transform(data['otu_counts'][2], opts.log_eps)
otu_table = get_log_transform(otu_table, opts.log_eps)
num_otu_hits = 0
fractional_values = False
max_val = -1
for val in otu_table.iterObservationData():
max_val = maximum(max_val, val.max())
# the data cannot be of mixed types: if one is float, all are float
fractional_values = (max_val.dtype.name == 'float32' or max_val.dtype.name == 'float64')
if fractional_values and max_val <= 1:
if num_otu_hits > 0:
print "Warning: OTU table appears to be using relative abundances",\
"and num_otu_hits was set to %d. Setting num_otu_hits to 0."\
%(num_otu_hits)
num_otu_hits = 0
filepath=opts.otu_table_fp
filename=filepath.strip().split('/')[-1].split('.')[0]
dir_path = opts.output_dir
create_dir(dir_path)
js_dir_path = os.path.join(dir_path,'js')
create_dir(js_dir_path)
qiime_dir=get_qiime_project_dir()
js_path=os.path.join(qiime_dir,'qiime/support_files/js')
shutil.copyfile(os.path.join(js_path,'overlib.js'), os.path.join(js_dir_path,'overlib.js'))
shutil.copyfile(os.path.join(js_path,'otu_count_display.js'), os.path.join(js_dir_path,'otu_count_display.js'))
shutil.copyfile(os.path.join(js_path,'jquery.js'), os.path.join(js_dir_path,'jquery.js'))
shutil.copyfile(os.path.join(js_path,'jquery.tablednd_0_5.js'), os.path.join(js_dir_path,'jquery.tablednd_0_5.js'))
# load tree for sorting OTUs
ordered_otu_names = None
if not opts.tree is None:
try:
f = open(opts.tree, 'U')
except (TypeError, IOError):
raise TreeMissingError, \
"Couldn't read tree file at path: %s" % tree_source
tree = parse_newick(f, PhyloNode)
f.close()
ordered_otu_names = [tip.Name for tip in tree.iterTips()]
ordered_sample_names = None
# load tree for sorting Samples
if not opts.sample_tree is None:
try:
f = open(opts.sample_tree, 'U')
except (TypeError, IOError):
raise TreeMissingError, \
"Couldn't read tree file at path: %s" % tree_source
tree = parse_newick(f, PhyloNode)
f.close()
ordered_sample_names = [tip.Name for tip in tree.iterTips()]
# if there's no sample tree, load sample map for sorting samples
elif not opts.map_fname is None:
lines = open(opts.map_fname,'U').readlines()
map = parse_mapping_file(lines)[0]
ordered_sample_names = [row[0] for row in map]
#data['otu_order'] = ordered_otu_names
#data['sample_order'] = ordered_sample_names
try:
action = generate_heatmap_plots
except NameError:
action = None
#Place this outside try/except so we don't mask NameError in action
if action:
action(num_otu_hits,otu_table, ordered_otu_names, ordered_sample_names,
dir_path,js_dir_path,filename, fractional_values)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
data = {}
#Open and get coord data
data['otu_counts'] = list(get_otu_counts(opts.otu_table_fp, data))
# determine whether fractional values are present in OTU table
if opts.log_transform:
if not opts.log_eps is None and opts.log_eps <= 0:
print "Parameter 'log_eps' must be positive. Value was", opts.log_eps
exit(1)
data['otu_counts'][2] = get_log_transform(data['otu_counts'][2], opts.log_eps)
opts.num_otu_hits = 0
# test: if using relative abundances, and opts.num_otu_hits > 0
# print warning and set to 0
fractional_values = ((data['otu_counts'][2] > 0) & \
(data['otu_counts'][2] < 1)).any()
if fractional_values and (data['otu_counts'][2]).max() <= 1:
if opts.num_otu_hits > 0:
print "Warning: OTU table appears to be using relative abundances",\
"and num_otu_hits was set to %d. Setting num_otu_hits to 0."\
%(opts.num_otu_hits)
opts.num_otu_hits = 0
filepath=opts.otu_table_fp
filename=filepath.strip().split('/')[-1].split('.')[0]
if opts.output_dir:
if os.path.exists(opts.output_dir):
dir_path=opts.output_dir
else:
try:
os.mkdir(opts.output_dir)
dir_path=opts.output_dir
except OSError:
pass
else:
dir_path='./'
js_dir_path = os.path.join(dir_path,'js')
try:
os.mkdir(js_dir_path)
except OSError:
pass
qiime_dir=get_qiime_project_dir()
js_path=os.path.join(qiime_dir,'qiime/support_files/js')
shutil.copyfile(os.path.join(js_path,'overlib.js'), os.path.join(js_dir_path,'overlib.js'))
shutil.copyfile(os.path.join(js_path,'otu_count_display.js'), os.path.join(js_dir_path,'otu_count_display.js'))
shutil.copyfile(os.path.join(js_path,'jquery.js'), os.path.join(js_dir_path,'jquery.js'))
shutil.copyfile(os.path.join(js_path,'jquery.tablednd_0_5.js'), os.path.join(js_dir_path,'jquery.tablednd_0_5.js'))
# load tree for sorting OTUs
ordered_otu_names = None
if not opts.tree is None:
try:
f = open(opts.tree, 'U')
except (TypeError, IOError):
raise TreeMissingError, \
"Couldn't read tree file at path: %s" % tree_source
tree = parse_newick(f, PhyloNode)
f.close()
ordered_otu_names = [tip.Name for tip in tree.iterTips()]
ordered_sample_names = None
# load tree for sorting Samples
if not opts.sample_tree is None:
try:
f = open(opts.sample_tree, 'U')
except (TypeError, IOError):
raise TreeMissingError, \
"Couldn't read tree file at path: %s" % tree_source
tree = parse_newick(f, PhyloNode)
f.close()
ordered_sample_names = [tip.Name for tip in tree.iterTips()]
# if there's no sample tree, load sample map for sorting samples
elif not opts.map_fname is None:
lines = open(opts.map_fname,'U').readlines()
map = parse_mapping_file(lines)[0]
ordered_sample_names = [row[0] for row in map]
data['otu_order'] = ordered_otu_names
data['sample_order'] = ordered_sample_names
try:
action = generate_heatmap_plots
except NameError:
action = None
#Place this outside try/except so we don't mask NameError in action
if action:
action(opts,data, dir_path,js_dir_path,filename, fractional_values)
