def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
otu_table_fp = opts.biom_fp
map_fp = opts.map_fp
output_dir = opts.output_dir
scolors = opts.scolors.split(',')
ocolors = opts.ocolors.split(',')
sshapes = opts.sshapes.split(',')
oshapes = opts.oshapes.split(',')
ssizes = opts.ssizes.split(',')
osizes = opts.osizes.split(',')
md_fields = opts.md_fields.split(',')
# check that the otu fields asked for are available
shared_options = ['NodeType', 'Abundance']
if not all(
[i in md_fields + shared_options for i in ocolors + oshapes + osizes]):
option_parser.error('The fields specified for observation colors, '
'sizes, or shapes are not in either the shared '
'options (NodeType,Abundance) or the supplied '
'md_fields. These fields must be a subset of the '
'union of these sets. Have you passed ocolors, '
'osizes or oshapes that are not in the md_fields?')
# check that the sample fields asked for are available. mapping file
# elements should all have same metadata keys
sopts = parse_mapping_file_to_dict(map_fp)[0].items()[0][1].keys()
if not all(
[i in sopts + shared_options for i in scolors + sshapes + ssizes]):
option_parser.error('The fields specified for sample colors, sizes, '
'or shapes are not in either the shared options '
'(NodeType,Abundance) or the supplied mapping '
'file. These fields must be a subset of the union '
'of these sets. Have you passed scolors, ssizes '
'or sshapes that are not in the mapping file '
'headers?')
# actual compuation begins
try:
create_dir(output_dir, fail_on_exist=True)
except OSError:
option_parser.error('Directory already exists. Will not overwrite.')
bt = load_table(otu_table_fp)
pmf = parse_mapping_file_to_dict(map_fp)[0] # [1] is comments, don't need
sample_node_table = make_sample_node_table(bt, pmf)
otu_node_table = make_otu_node_table(bt, opts.observation_md_header_key,
md_fields)
node_attr_table = make_node_attr_table(otu_node_table, sample_node_table,
scolors, ocolors, ssizes, osizes,
sshapes, oshapes)
edge_table = make_edge_table(bt)
_write_table(sample_node_table,
os.path.join(output_dir, 'SampleNodeTable.txt'))
_write_table(otu_node_table, os.path.join(output_dir, 'OTUNodeTable.txt'))
_write_table(node_attr_table, os.path.join(output_dir,
'NodeAttrTable.txt'))
_write_table(edge_table, os.path.join(output_dir, 'EdgeTable.txt'))
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
otu_table_fp = opts.biom_fp
map_fp = opts.map_fp
output_dir = opts.output_dir
taxonomy_key = opts.observation_md_header_key
scolors = opts.scolors.split(',')
ocolors = opts.ocolors.split(',')
sshapes = opts.sshapes.split(',')
oshapes = opts.oshapes.split(',')
ssizes = opts.ssizes.split(',')
osizes = opts.osizes.split(',')
md_fields = opts.md_fields.split(',')
# check that the otu fields asked for are available
shared_options = ['NodeType','Abundance']
if not all([i in md_fields+shared_options for i in ocolors+oshapes+osizes]):
option_parser.error('The fields specified for observation colors, sizes, or '+\
'shapes are not in either the shared options (NodeType,Abundance)'+\
' or the supplied md_fields. These fields must be a subset of '+\
'the union of these sets. Have you passed ocolors, osizes or '+\
'oshapes that are not in the md_fields?')
# check that the sample fields asked for are available. mapping file
# elements should all have same metadata keys
sopts = parse_mapping_file_to_dict(map_fp)[0].items()[0][1].keys()
if not all([i in sopts+shared_options for i in scolors+sshapes+ssizes]):
option_parser.error('The fields specified for sample colors, sizes, or '+\
'shapes are not in either the shared options (NodeType,Abundance)'+\
' or the supplied mapping file. These fields must be a subset of '+\
'the union of these sets. Have you passed scolors, ssizes or '+\
'sshapes that are not in the mapping file headers?')
# actual compuation begins
try:
create_dir(output_dir, fail_on_exist=True)
except OSError:
option_parser.error('Directory already exists. Will not overwrite.')
bt = parse_biom_table(open(otu_table_fp))
pmf = parse_mapping_file_to_dict(map_fp)[0] # [1] is comments, don't need
sample_node_table = make_sample_node_table(bt, pmf)
otu_node_table = make_otu_node_table(bt, opts.observation_md_header_key,
md_fields)
node_attr_table = make_node_attr_table(otu_node_table, sample_node_table,
scolors, ocolors, ssizes, osizes, sshapes, oshapes)
edge_table = make_edge_table(bt)
_write_table(sample_node_table, os.path.join(output_dir,'SampleNodeTable.txt'))
_write_table(otu_node_table, os.path.join(output_dir,'OTUNodeTable.txt'))
_write_table(node_attr_table, os.path.join(output_dir,'NodeAttrTable.txt'))
_write_table(edge_table, os.path.join(output_dir,'EdgeTable.txt'))
def test_make_otu_node_table(self):
'''Test that make_otu_node_table makes accurate calculations.'''
# test when length of md_fields and length of split taxonomy wouldn't
# agree when md type is list or string.
bt1 = parse_biom_table(BIOM_STRING_1)
md_key = 'taxonomy'
md_fields = ['k']
obs = make_otu_node_table(bt1, md_key, md_fields)
exp = [
'#NodeID\tNodeType\tAbundance\tk',
'o1\totu\t15.0\tk__Bacteria',
'o2\totu\t40.0\tk__Bacteria',
'o3\totu\t65.0\tk__Bacteria',
'o4\totu\t90.0\tk__Bacteria',
'o5\totu\t115.0\tk__Bacteria',
'o6\totu\t140.0\tk__Bacteria',
'o7\totu\t165.0\tk__Bacteria',
'o8\totu\t190.0\tk__Bacteria']
self.assertEqual(obs, exp)
md_fields = ['k', '1', '2', '3', '4', '5', '6']
obs = make_otu_node_table(bt1, md_key, md_fields)
exp = [
'#NodeID\tNodeType\tAbundance\tk\t1\t2\t3\t4\t5\t6',
'o1\totu\t15.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae\tOther\tOther',
'o2\totu\t40.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1\tOther\tOther',
'o3\totu\t65.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1\tOther\tOther',
'o4\totu\t90.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2\tOther\tOther',
'o5\totu\t115.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2\tOther\tOther',
'o6\totu\t140.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae\tOther\tOther',
'o7\totu\t165.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae\tOther\tOther',
'o8\totu\t190.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae\tOther\tOther']
# test when the length of the md_fields is correct
md_fields = ['k', 'p', 'c', 'o', 'f']
obs_bt1 = make_otu_node_table(bt1, md_key, md_fields)
exp_bt1 = \
['#NodeID\tNodeType\tAbundance\tk\tp\tc\to\tf',
'o1\totu\t15.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae',
'o2\totu\t40.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o3\totu\t65.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o4\totu\t90.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o5\totu\t115.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o6\totu\t140.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o7\totu\t165.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o8\totu\t190.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae']
self.assertEqual(obs_bt1, exp_bt1)
md_fields = ['k', 'p', 'c', 'o', 'f']
bt2 = parse_biom_table(BIOM_STRING_3)
obs_bt2 = make_otu_node_table(bt2, md_key, md_fields)
exp_bt2 = \
['#NodeID\tNodeType\tAbundance\tk\tp\tc\to\tf',
'o1\totu\t12.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae',
'o2\totu\t27.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o3\totu\t42.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o4\totu\t57.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o5\totu\t72.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o6\totu\t87.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o7\totu\t102.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o8\totu\t117.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae']
self.assertEqual(obs_bt2, exp_bt2)
# test when the md is of type dict and fields are correct
bt = parse_biom_table(BIOM_STRING_4)
md_fields = ['kingdom', 'phylum', 'class', 'order', 'family']
obs_bt = make_otu_node_table(bt, md_key, md_fields)
exp_bt = \
['#NodeID\tNodeType\tAbundance\tkingdom\tphylum\tclass\torder\tfamily',
'o1\totu\t15.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae',
'o2\totu\t40.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o3\totu\t65.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o4\totu\t90.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o5\totu\t115.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o6\totu\t140.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o7\totu\t165.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o8\totu\t190.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae']
self.assertEqual(obs_bt, exp_bt)
# test that it raises an error when md_fields not found in md_dict
md_fields = ['KINGDOM', 'phylum', 'class', 'order', 'family']
self.assertRaises(
ValueError,
make_otu_node_table,
bt,
md_key,
md_fields)
# test that it doesn't error when md_fields is subset of md_dict
md_fields = ['phylum', 'class', 'order', 'family']
obs_bt = make_otu_node_table(bt, md_key, md_fields)
exp_bt = \
['#NodeID\tNodeType\tAbundance\tphylum\tclass\torder\tfamily',
'o1\totu\t15.0\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae',
'o2\totu\t40.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o3\totu\t65.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o4\totu\t90.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o5\totu\t115.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o6\totu\t140.0\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o7\totu\t165.0\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o8\totu\t190.0\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae']
self.assertEqual(obs_bt, exp_bt)
# test when the md is type defaultdict
bt = parse_biom_table(BIOM_STRING_5)
# test that it raises an error when md_fields not found in md_dict
md_fields = ['KINGDOM', 'phylum', 'class', 'order', 'family']
self.assertRaises(
ValueError,
make_otu_node_table,
bt,
md_key,
md_fields)
# test that it doesn't error when md_fields is subset of md_dict
md_fields = ['phylum', 'class', 'order', 'family']
obs_bt = make_otu_node_table(bt, md_key, md_fields)
exp_bt = \
['#NodeID\tNodeType\tAbundance\tphylum\tclass\torder\tfamily',
'o1\totu\t15.0\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae',
'o2\totu\t40.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o3\totu\t65.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o4\totu\t90.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o5\totu\t115.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o6\totu\t140.0\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o7\totu\t165.0\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o8\totu\t190.0\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae']
self.assertEqual(obs_bt, exp_bt)
def test_node_attr_table(self):
'''Test that node_attr_table is made correctly.'''
# test color,size,shape with shared attributes: NodeType, Abundance
bt = parse_biom_table(BIOM_STRING_1)
mf_dict = parse_mapping_file_to_dict(MF_LINES.split('\n'))[0]
sample_node_lines = make_sample_node_table(bt, mf_dict)
md_key = 'taxonomy'
md_fields = ['k', 'p', 'c', 'o', 'f']
otu_node_lines = make_otu_node_table(bt, md_key, md_fields)
scolor = ['NodeType']
ocolor = ['NodeType']
sshape = ['NodeType', 'Abundance']
oshape = ['NodeType']
ssize = ['Abundance']
osize = ['Abundance', 'NodeType']
obs_out = make_node_attr_table(otu_node_lines, sample_node_lines,
scolor, ocolor, ssize, osize, sshape, oshape)
exp_out = \
['#NodeID\tNodeType\tAbundance\tColor\tSize\tShape',
's1\tsample\t148.0\tsample\t148.0\tsample_148.0',
's2\tsample\t156.0\tsample\t156.0\tsample_156.0',
's3\tsample\t164.0\tsample\t164.0\tsample_164.0',
's4\tsample\t172.0\tsample\t172.0\tsample_172.0',
's5\tsample\t180.0\tsample\t180.0\tsample_180.0',
'o1\totu\t15.0\totu\t15.0_otu\totu',
'o2\totu\t40.0\totu\t40.0_otu\totu',
'o3\totu\t65.0\totu\t65.0_otu\totu',
'o4\totu\t90.0\totu\t90.0_otu\totu',
'o5\totu\t115.0\totu\t115.0_otu\totu',
'o6\totu\t140.0\totu\t140.0_otu\totu',
'o7\totu\t165.0\totu\t165.0_otu\totu',
'o8\totu\t190.0\totu\t190.0_otu\totu']
# order different because computed by hand. As long as sets the same
# we are confident they are the same
self.assertEqual(set(obs_out), set(exp_out))
# test color,size,shape with some shared and some non-shared attrs
md_key = 'taxonomy'
md_fields = ['k', 'p', 'c', 'o', 'f']
otu_node_lines = make_otu_node_table(bt, md_key, md_fields)
scolor = ['NodeType', 'Diet']
ocolor = ['k', 'p']
sshape = ['Treatment', 'Abundance']
oshape = ['NodeType', 'o']
ssize = ['Abundance']
osize = ['Abundance', 'NodeType']
obs_out = make_node_attr_table(otu_node_lines, sample_node_lines,
scolor, ocolor, ssize, osize, sshape, oshape)
exp_out = \
['#NodeID\tNodeType\tAbundance\tColor\tSize\tShape',
's1\tsample\t148.0\tsample_hf\t148.0\tpre_148.0',
's2\tsample\t156.0\tsample_lf\t156.0\tpre_156.0',
's3\tsample\t164.0\tsample_hf\t164.0\tpre_164.0',
's4\tsample\t172.0\tsample_lf\t172.0\tpost_172.0',
's5\tsample\t180.0\tsample_mf\t180.0\tpost_180.0',
'o1\totu\t15.0\tk__Bacteria_p__Firmicutes\t15.0_otu\totu_o__Clostridiales',
'o2\totu\t40.0\tk__Bacteria_p__Firmicutes\t40.0_otu\totu_o__Clostridiales',
'o3\totu\t65.0\tk__Bacteria_p__Firmicutes\t65.0_otu\totu_o__Clostridiales',
'o4\totu\t90.0\tk__Bacteria_p__Firmicutes\t90.0_otu\totu_o__Clostridiales',
'o5\totu\t115.0\tk__Bacteria_p__Firmicutes\t115.0_otu\totu_o__Clostridiales',
'o6\totu\t140.0\tk__Bacteria_p__Firmicutes\t140.0_otu\totu_o__Clostri3',
'o7\totu\t165.0\tk__Bacteria_p__Firmicutes\t165.0_otu\totu_o__Clostri3',
'o8\totu\t190.0\tk__Bacteria_p__Firmicutes\t190.0_otu\totu_o__Clostridiales']
# order different because computed by hand. As long as sets the same
# we are confident they are the same
self.assertEqual(set(obs_out), set(exp_out))
def test_make_otu_node_table(self):
'''Test that make_otu_node_table makes accurate calculations.'''
# test when length of md_fields and length of split taxonomy wouldn't
# agree when md type is list or string.
bt1 = parse_biom_table(BIOM_STRING_1)
md_key = 'taxonomy'
md_fields = ['k']
obs = make_otu_node_table(bt1, md_key, md_fields)
exp = [
'#NodeID\tNodeType\tAbundance\tk', 'o1\totu\t15.0\tk__Bacteria',
'o2\totu\t40.0\tk__Bacteria', 'o3\totu\t65.0\tk__Bacteria',
'o4\totu\t90.0\tk__Bacteria', 'o5\totu\t115.0\tk__Bacteria',
'o6\totu\t140.0\tk__Bacteria', 'o7\totu\t165.0\tk__Bacteria',
'o8\totu\t190.0\tk__Bacteria'
]
self.assertEqual(obs, exp)
md_fields = ['k', '1', '2', '3', '4', '5', '6']
obs = make_otu_node_table(bt1, md_key, md_fields)
exp = [
'#NodeID\tNodeType\tAbundance\tk\t1\t2\t3\t4\t5\t6',
'o1\totu\t15.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae\tOther\tOther',
'o2\totu\t40.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1\tOther\tOther',
'o3\totu\t65.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1\tOther\tOther',
'o4\totu\t90.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2\tOther\tOther',
'o5\totu\t115.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2\tOther\tOther',
'o6\totu\t140.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae\tOther\tOther',
'o7\totu\t165.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae\tOther\tOther',
'o8\totu\t190.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae\tOther\tOther'
]
# test when the length of the md_fields is correct
md_fields = ['k', 'p', 'c', 'o', 'f']
obs_bt1 = make_otu_node_table(bt1, md_key, md_fields)
exp_bt1 = \
['#NodeID\tNodeType\tAbundance\tk\tp\tc\to\tf',
'o1\totu\t15.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae',
'o2\totu\t40.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o3\totu\t65.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o4\totu\t90.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o5\totu\t115.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o6\totu\t140.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o7\totu\t165.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o8\totu\t190.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae']
self.assertEqual(obs_bt1, exp_bt1)
md_fields = ['k', 'p', 'c', 'o', 'f']
bt2 = parse_biom_table(BIOM_STRING_3)
obs_bt2 = make_otu_node_table(bt2, md_key, md_fields)
exp_bt2 = \
['#NodeID\tNodeType\tAbundance\tk\tp\tc\to\tf',
'o1\totu\t12.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae',
'o2\totu\t27.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o3\totu\t42.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o4\totu\t57.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o5\totu\t72.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o6\totu\t87.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o7\totu\t102.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o8\totu\t117.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae']
self.assertEqual(obs_bt2, exp_bt2)
# test when the md is of type dict and fields are correct
bt = parse_biom_table(BIOM_STRING_4)
md_fields = ['kingdom', 'phylum', 'class', 'order', 'family']
obs_bt = make_otu_node_table(bt, md_key, md_fields)
exp_bt = \
['#NodeID\tNodeType\tAbundance\tkingdom\tphylum\tclass\torder\tfamily',
'o1\totu\t15.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae',
'o2\totu\t40.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o3\totu\t65.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o4\totu\t90.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o5\totu\t115.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o6\totu\t140.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o7\totu\t165.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o8\totu\t190.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae']
self.assertEqual(obs_bt, exp_bt)
# test that it raises an error when md_fields not found in md_dict
md_fields = ['KINGDOM', 'phylum', 'class', 'order', 'family']
self.assertRaises(ValueError, make_otu_node_table, bt, md_key,
md_fields)
# test that it doesn't error when md_fields is subset of md_dict
md_fields = ['phylum', 'class', 'order', 'family']
obs_bt = make_otu_node_table(bt, md_key, md_fields)
exp_bt = \
['#NodeID\tNodeType\tAbundance\tphylum\tclass\torder\tfamily',
'o1\totu\t15.0\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae',
'o2\totu\t40.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o3\totu\t65.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o4\totu\t90.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o5\totu\t115.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o6\totu\t140.0\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o7\totu\t165.0\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o8\totu\t190.0\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae']
self.assertEqual(obs_bt, exp_bt)
# test when the md is type defaultdict
bt = parse_biom_table(BIOM_STRING_5)
# test that it raises an error when md_fields not found in md_dict
md_fields = ['KINGDOM', 'phylum', 'class', 'order', 'family']
self.assertRaises(ValueError, make_otu_node_table, bt, md_key,
md_fields)
# test that it doesn't error when md_fields is subset of md_dict
md_fields = ['phylum', 'class', 'order', 'family']
obs_bt = make_otu_node_table(bt, md_key, md_fields)
exp_bt = \
['#NodeID\tNodeType\tAbundance\tphylum\tclass\torder\tfamily',
'o1\totu\t15.0\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae',
'o2\totu\t40.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o3\totu\t65.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1',
'o4\totu\t90.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o5\totu\t115.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2',
'o6\totu\t140.0\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o7\totu\t165.0\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae',
'o8\totu\t190.0\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae']
self.assertEqual(obs_bt, exp_bt)
def test_node_attr_table(self):
'''Test that node_attr_table is made correctly.'''
# test color,size,shape with shared attributes: NodeType, Abundance
bt = parse_biom_table(BIOM_STRING_1)
mf_dict = parse_mapping_file_to_dict(MF_LINES.split('\n'))[0]
sample_node_lines = make_sample_node_table(bt, mf_dict)
md_key = 'taxonomy'
md_fields = ['k', 'p', 'c', 'o', 'f']
otu_node_lines = make_otu_node_table(bt, md_key, md_fields)
scolor = ['NodeType']
ocolor = ['NodeType']
sshape = ['NodeType', 'Abundance']
oshape = ['NodeType']
ssize = ['Abundance']
osize = ['Abundance', 'NodeType']
obs_out = make_node_attr_table(otu_node_lines, sample_node_lines,
scolor, ocolor, ssize, osize, sshape,
oshape)
exp_out = \
['#NodeID\tNodeType\tAbundance\tColor\tSize\tShape',
's1\tsample\t148.0\tsample\t148.0\tsample_148.0',
's2\tsample\t156.0\tsample\t156.0\tsample_156.0',
's3\tsample\t164.0\tsample\t164.0\tsample_164.0',
's4\tsample\t172.0\tsample\t172.0\tsample_172.0',
's5\tsample\t180.0\tsample\t180.0\tsample_180.0',
'o1\totu\t15.0\totu\t15.0_otu\totu',
'o2\totu\t40.0\totu\t40.0_otu\totu',
'o3\totu\t65.0\totu\t65.0_otu\totu',
'o4\totu\t90.0\totu\t90.0_otu\totu',
'o5\totu\t115.0\totu\t115.0_otu\totu',
'o6\totu\t140.0\totu\t140.0_otu\totu',
'o7\totu\t165.0\totu\t165.0_otu\totu',
'o8\totu\t190.0\totu\t190.0_otu\totu']
# order different because computed by hand. As long as sets the same
# we are confident they are the same
self.assertEqual(set(obs_out), set(exp_out))
# test color,size,shape with some shared and some non-shared attrs
md_key = 'taxonomy'
md_fields = ['k', 'p', 'c', 'o', 'f']
otu_node_lines = make_otu_node_table(bt, md_key, md_fields)
scolor = ['NodeType', 'Diet']
ocolor = ['k', 'p']
sshape = ['Treatment', 'Abundance']
oshape = ['NodeType', 'o']
ssize = ['Abundance']
osize = ['Abundance', 'NodeType']
obs_out = make_node_attr_table(otu_node_lines, sample_node_lines,
scolor, ocolor, ssize, osize, sshape,
oshape)
exp_out = \
['#NodeID\tNodeType\tAbundance\tColor\tSize\tShape',
's1\tsample\t148.0\tsample_hf\t148.0\tpre_148.0',
's2\tsample\t156.0\tsample_lf\t156.0\tpre_156.0',
's3\tsample\t164.0\tsample_hf\t164.0\tpre_164.0',
's4\tsample\t172.0\tsample_lf\t172.0\tpost_172.0',
's5\tsample\t180.0\tsample_mf\t180.0\tpost_180.0',
'o1\totu\t15.0\tk__Bacteria_p__Firmicutes\t15.0_otu\totu_o__Clostridiales',
'o2\totu\t40.0\tk__Bacteria_p__Firmicutes\t40.0_otu\totu_o__Clostridiales',
'o3\totu\t65.0\tk__Bacteria_p__Firmicutes\t65.0_otu\totu_o__Clostridiales',
'o4\totu\t90.0\tk__Bacteria_p__Firmicutes\t90.0_otu\totu_o__Clostridiales',
'o5\totu\t115.0\tk__Bacteria_p__Firmicutes\t115.0_otu\totu_o__Clostridiales',
'o6\totu\t140.0\tk__Bacteria_p__Firmicutes\t140.0_otu\totu_o__Clostri3',
'o7\totu\t165.0\tk__Bacteria_p__Firmicutes\t165.0_otu\totu_o__Clostri3',
'o8\totu\t190.0\tk__Bacteria_p__Firmicutes\t190.0_otu\totu_o__Clostridiales']
# order different because computed by hand. As long as sets the same
# we are confident they are the same
self.assertEqual(set(obs_out), set(exp_out))
def test_make_otu_node_table(self):
"""Test that make_otu_node_table makes accurate calculations."""
# test when length of md_fields and length of split taxonomy wouldn't
# agree when md type is list or string.
bt1 = parse_biom_table(BIOM_STRING_1)
md_key = "taxonomy"
md_fields = ["k"]
obs = make_otu_node_table(bt1, md_key, md_fields)
exp = [
"#NodeID\tNodeType\tAbundance\tk",
"o1\totu\t15.0\tk__Bacteria",
"o2\totu\t40.0\tk__Bacteria",
"o3\totu\t65.0\tk__Bacteria",
"o4\totu\t90.0\tk__Bacteria",
"o5\totu\t115.0\tk__Bacteria",
"o6\totu\t140.0\tk__Bacteria",
"o7\totu\t165.0\tk__Bacteria",
"o8\totu\t190.0\tk__Bacteria",
]
self.assertEqual(obs, exp)
md_fields = ["k", "1", "2", "3", "4", "5", "6"]
obs = make_otu_node_table(bt1, md_key, md_fields)
exp = [
"#NodeID\tNodeType\tAbundance\tk\t1\t2\t3\t4\t5\t6",
"o1\totu\t15.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae\tOther\tOther",
"o2\totu\t40.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1\tOther\tOther",
"o3\totu\t65.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1\tOther\tOther",
"o4\totu\t90.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2\tOther\tOther",
"o5\totu\t115.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2\tOther\tOther",
"o6\totu\t140.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae\tOther\tOther",
"o7\totu\t165.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae\tOther\tOther",
"o8\totu\t190.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae\tOther\tOther",
]
# test when the length of the md_fields is correct
md_fields = ["k", "p", "c", "o", "f"]
obs_bt1 = make_otu_node_table(bt1, md_key, md_fields)
exp_bt1 = [
"#NodeID\tNodeType\tAbundance\tk\tp\tc\to\tf",
"o1\totu\t15.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae",
"o2\totu\t40.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1",
"o3\totu\t65.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1",
"o4\totu\t90.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2",
"o5\totu\t115.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2",
"o6\totu\t140.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae",
"o7\totu\t165.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae",
"o8\totu\t190.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae",
]
self.assertEqual(obs_bt1, exp_bt1)
md_fields = ["k", "p", "c", "o", "f"]
bt2 = parse_biom_table(BIOM_STRING_3)
obs_bt2 = make_otu_node_table(bt2, md_key, md_fields)
exp_bt2 = [
"#NodeID\tNodeType\tAbundance\tk\tp\tc\to\tf",
"o1\totu\t12.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae",
"o2\totu\t27.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1",
"o3\totu\t42.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1",
"o4\totu\t57.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2",
"o5\totu\t72.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2",
"o6\totu\t87.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae",
"o7\totu\t102.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae",
"o8\totu\t117.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae",
]
self.assertEqual(obs_bt2, exp_bt2)
# test when the md is of type dict and fields are correct
bt = parse_biom_table(BIOM_STRING_4)
md_fields = ["kingdom", "phylum", "class", "order", "family"]
obs_bt = make_otu_node_table(bt, md_key, md_fields)
exp_bt = [
"#NodeID\tNodeType\tAbundance\tkingdom\tphylum\tclass\torder\tfamily",
"o1\totu\t15.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae",
"o2\totu\t40.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1",
"o3\totu\t65.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1",
"o4\totu\t90.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2",
"o5\totu\t115.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2",
"o6\totu\t140.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae",
"o7\totu\t165.0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae",
"o8\totu\t190.0\tk__Bacteria\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae",
]
self.assertEqual(obs_bt, exp_bt)
# test that it raises an error when md_fields not found in md_dict
md_fields = ["KINGDOM", "phylum", "class", "order", "family"]
self.assertRaises(ValueError, make_otu_node_table, bt, md_key, md_fields)
# test that it doesn't error when md_fields is subset of md_dict
md_fields = ["phylum", "class", "order", "family"]
obs_bt = make_otu_node_table(bt, md_key, md_fields)
exp_bt = [
"#NodeID\tNodeType\tAbundance\tphylum\tclass\torder\tfamily",
"o1\totu\t15.0\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae",
"o2\totu\t40.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1",
"o3\totu\t65.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1",
"o4\totu\t90.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2",
"o5\totu\t115.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2",
"o6\totu\t140.0\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae",
"o7\totu\t165.0\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae",
"o8\totu\t190.0\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae",
]
self.assertEqual(obs_bt, exp_bt)
# test when the md is type defaultdict
bt = parse_biom_table(BIOM_STRING_5)
# test that it raises an error when md_fields not found in md_dict
md_fields = ["KINGDOM", "phylum", "class", "order", "family"]
self.assertRaises(ValueError, make_otu_node_table, bt, md_key, md_fields)
# test that it doesn't error when md_fields is subset of md_dict
md_fields = ["phylum", "class", "order", "family"]
obs_bt = make_otu_node_table(bt, md_key, md_fields)
exp_bt = [
"#NodeID\tNodeType\tAbundance\tphylum\tclass\torder\tfamily",
"o1\totu\t15.0\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae",
"o2\totu\t40.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1",
"o3\totu\t65.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos1",
"o4\totu\t90.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2",
"o5\totu\t115.0\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnos2",
"o6\totu\t140.0\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae",
"o7\totu\t165.0\tp__Firmicutes\tc__Clostridia\to__Clostri3\tf__Lachnospiraceae",
"o8\totu\t190.0\tp__Firmicutes\tc__Clost5\to__Clostridiales\tf__Lachnospiraceae",
]
self.assertEqual(obs_bt, exp_bt)
def test_node_attr_table(self):
"""Test that node_attr_table is made correctly."""
# test color,size,shape with shared attributes: NodeType, Abundance
bt = parse_biom_table(BIOM_STRING_1)
mf_dict = parse_mapping_file_to_dict(MF_LINES.split("\n"))[0]
sample_node_lines = make_sample_node_table(bt, mf_dict)
md_key = "taxonomy"
md_fields = ["k", "p", "c", "o", "f"]
otu_node_lines = make_otu_node_table(bt, md_key, md_fields)
scolor = ["NodeType"]
ocolor = ["NodeType"]
sshape = ["NodeType", "Abundance"]
oshape = ["NodeType"]
ssize = ["Abundance"]
osize = ["Abundance", "NodeType"]
obs_out = make_node_attr_table(otu_node_lines, sample_node_lines, scolor, ocolor, ssize, osize, sshape, oshape)
exp_out = [
"#NodeID\tNodeType\tAbundance\tColor\tSize\tShape",
"s1\tsample\t148.0\tsample\t148.0\tsample_148.0",
"s2\tsample\t156.0\tsample\t156.0\tsample_156.0",
"s3\tsample\t164.0\tsample\t164.0\tsample_164.0",
"s4\tsample\t172.0\tsample\t172.0\tsample_172.0",
"s5\tsample\t180.0\tsample\t180.0\tsample_180.0",
"o1\totu\t15.0\totu\t15.0_otu\totu",
"o2\totu\t40.0\totu\t40.0_otu\totu",
"o3\totu\t65.0\totu\t65.0_otu\totu",
"o4\totu\t90.0\totu\t90.0_otu\totu",
"o5\totu\t115.0\totu\t115.0_otu\totu",
"o6\totu\t140.0\totu\t140.0_otu\totu",
"o7\totu\t165.0\totu\t165.0_otu\totu",
"o8\totu\t190.0\totu\t190.0_otu\totu",
]
# order different because computed by hand. As long as sets the same
# we are confident they are the same
self.assertEqual(set(obs_out), set(exp_out))
# test color,size,shape with some shared and some non-shared attrs
md_key = "taxonomy"
md_fields = ["k", "p", "c", "o", "f"]
otu_node_lines = make_otu_node_table(bt, md_key, md_fields)
scolor = ["NodeType", "Diet"]
ocolor = ["k", "p"]
sshape = ["Treatment", "Abundance"]
oshape = ["NodeType", "o"]
ssize = ["Abundance"]
osize = ["Abundance", "NodeType"]
obs_out = make_node_attr_table(otu_node_lines, sample_node_lines, scolor, ocolor, ssize, osize, sshape, oshape)
exp_out = [
"#NodeID\tNodeType\tAbundance\tColor\tSize\tShape",
"s1\tsample\t148.0\tsample_hf\t148.0\tpre_148.0",
"s2\tsample\t156.0\tsample_lf\t156.0\tpre_156.0",
"s3\tsample\t164.0\tsample_hf\t164.0\tpre_164.0",
"s4\tsample\t172.0\tsample_lf\t172.0\tpost_172.0",
"s5\tsample\t180.0\tsample_mf\t180.0\tpost_180.0",
"o1\totu\t15.0\tk__Bacteria_p__Firmicutes\t15.0_otu\totu_o__Clostridiales",
"o2\totu\t40.0\tk__Bacteria_p__Firmicutes\t40.0_otu\totu_o__Clostridiales",
"o3\totu\t65.0\tk__Bacteria_p__Firmicutes\t65.0_otu\totu_o__Clostridiales",
"o4\totu\t90.0\tk__Bacteria_p__Firmicutes\t90.0_otu\totu_o__Clostridiales",
"o5\totu\t115.0\tk__Bacteria_p__Firmicutes\t115.0_otu\totu_o__Clostridiales",
"o6\totu\t140.0\tk__Bacteria_p__Firmicutes\t140.0_otu\totu_o__Clostri3",
"o7\totu\t165.0\tk__Bacteria_p__Firmicutes\t165.0_otu\totu_o__Clostri3",
"o8\totu\t190.0\tk__Bacteria_p__Firmicutes\t190.0_otu\totu_o__Clostridiales",
]
# order different because computed by hand. As long as sets the same
# we are confident they are the same
self.assertEqual(set(obs_out), set(exp_out))
