def test_preprocess_otu_table_exceptions(self):
"""Check the exceptions are raised appropriately"""
# should raise an exception because the inputs contain a single row
with self.assertRaises(EmperorUnsupportedComputation):
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines = preprocess_otu_table(
self.otu_sample_ids, self.otu_table_broken, self.lineages_broken, self.coords, self.coords_header, 4
)
# some inputs are completely wrong but should still fail because the
# contingency table has one row only, hence scores cannot be computed
with self.assertRaises(EmperorUnsupportedComputation):
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines = preprocess_otu_table(
self.otu_sample_ids, self.otu_table_broken, [[]], self.coords, self.coords_header, 4
)
with self.assertRaises(EmperorUnsupportedComputation):
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines = preprocess_otu_table(
self.otu_sample_ids, array([]), self.lineages_broken, self.coords, self.coords_header, 4
)
def test_preprocess_otu_table_exceptions(self):
"""Check the exceptions are raised appropriately"""
# should raise an exception because the inputs contain a single row
with self.assertRaises(EmperorUnsupportedComputation):
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines =\
preprocess_otu_table(self.otu_sample_ids, self.otu_table_broken,
self.lineages_broken, self.coords, self.coords_header, 4)
# some inputs are completely wrong but should still fail because the
# contingency table has one row only, hence scores cannot be computed
with self.assertRaises(EmperorUnsupportedComputation):
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines =\
preprocess_otu_table(self.otu_sample_ids, self.otu_table_broken,
[[]], self.coords, self.coords_header, 4)
with self.assertRaises(EmperorUnsupportedComputation):
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines =\
preprocess_otu_table(self.otu_sample_ids, array([]),
self.lineages_broken, self.coords, self.coords_header, 4)
def test_preprocess_otu_table(self):
"""Check the coords and otu table are processed correctly"""
# processing only the four most prevalent taxa
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines =\
preprocess_otu_table(self.otu_sample_ids, self.otu_table,
self.lineages, self.coords, self.coords_header, 4)
assert_almost_equal(o_otu_coords, array([[ -6.71083200e-02,
1.05892642e-02, -5.26801821e-03, -1.31730322e-02, 3.15036935e-02,
-1.99712144e-02, 8.14445313e-03, -1.76632227e-02, -4.84141987e-09],
[ 9.65846961e-02, -1.64070839e-02, 1.68610695e-02, 1.03495979e-02,
-2.26223522e-02, 2.83763737e-02, 1.76116225e-05, 2.89253284e-02,
-4.84141987e-09], [-5.61881305e-04, 1.16341355e-02, -4.97196330e-02,
4.51141625e-02, -1.29353935e-01, -2.14114921e-02, -6.92988035e-02,
-6.27730937e-02, -4.84141987e-09], [-5.70985165e-02,
-1.09278921e-02, 8.49830390e-04, -1.91550282e-02, -4.22122952e-02,
7.75750297e-04, -1.18543093e-02, 3.31082777e-02, -4.84141987e-09]]))
assert_almost_equal(o_otu_table, array([[ 0.78767123, 0.45637584, 0.22,
0.39597315, 0.41610738, 0.20945946, 0.70068027, 0.89932886,
0.77333333], [0.14383562, 0.27516779, 0.65333333, 0.52348993,
0.38926174, 0.69594595, 0.28571429, 0.0738255, 0.19333333], [
0.03424658, 0.16107383, 0.02666667, 0.00671141, 0.14765101,
0.01351351, 0., 0.01342282, 0.00666667], [0.02739726, 0.04697987,
0.02, 0.04697987, 0.01, 0.02027027, 0.01360544, 0.01342282,
0.02666667]]))
self.assertEquals(o_otu_lineages, ['Root;k__Bacteria;p__Firmicutes',
'Root;k__Bacteria;p__Bacteroidetes',
'Root;k__Bacteria;p__Tenericutes', 'Root;k__Bacteria;Other'])
assert_almost_equal(o_prevalence, array([ 1., 0.66471926, 0.08193196,
0.04374296]))
self.assertEquals(lines, LINES)
# tests for correct outputs of empty inputs
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines =\
preprocess_otu_table([],[], [], self.coords, self.coords_header, 4)
self.assertEquals(o_otu_coords, [])
self.assertEquals(o_otu_table, [])
self.assertEquals(o_otu_lineages, [])
self.assertEquals(o_prevalence, [])
self.assertEquals(lines, '')
'that are not numeric, hence not suitable for \'--custom_axes\' nor'
' for \'--add_vectors\'. Try the \'--missing_custom_axes_values\' '
'option to fix these values.' % ', '.join(non_numeric_categories)))
# process the coordinates file first, preventing the case where the custom
# axes is not in the coloring categories i. e. in the --colory_by categories
coords_headers, coords_data, coords_eigenvalues, coords_pct, coords_low,\
coords_high, clones = preprocess_coords_file(coords_headers,coords_data,
coords_eigenvalues, coords_pct, header, mapping_data, custom_axes,
jackknifing_method=jackknifing_method, is_comparison=compare_plots,
pct_variation_below_one=pct_variation_below_one)
# process the otu table after processing the coordinates to get custom axes
# (when available) or any other change that occurred to the coordinates
otu_coords, otu_table, otu_lineages, otu_prevalence, lines =\
preprocess_otu_table(otu_sample_ids, otu_table, lineages,
coords_data, coords_headers, n_taxa_to_keep)
# remove the columns in the mapping file that are not informative taking
# into account the header names that were already authorized to be used
# and take care of concatenating the fields for the && merged columns
mapping_data, header = preprocess_mapping_file(mapping_data, header,
color_by_column_names, unique=not add_unique_columns, clones=clones)
# create the output directory before creating any other output
if not isdir(opts.output_dir):
makedirs(opts.output_dir)
fp_out = open(join(output_dir, 'index.html'),'w')
fp_out.write(emperor_autograph+'\n')
fp_out.write(EMPEROR_HEADER_HTML_STRING)
option_parser.error(('The following field(s): \'%s\' contain values '
'that are not numeric, hence not suitable for \'--custom_axes\' nor'
' for \'--add_vectors\'. Try the \'--missing_custom_axes_values\' '
'option to fix these values.' % ', '.join(non_numeric_categories)))
# process the coordinates file first, preventing the case where the custom
# axes is not in the coloring categories i. e. in the --colory_by categories
coords_headers, coords_data, coords_eigenvalues, coords_pct, coords_low,\
coords_high, clones = preprocess_coords_file(coords_headers,coords_data,
coords_eigenvalues, coords_pct, header, mapping_data, custom_axes,
jackknifing_method=jackknifing_method, is_comparison=compare_plots)
# process the otu table after processing the coordinates to get custom axes
# (when available) or any other change that occurred to the coordinates
otu_coords, otu_table, otu_lineages, otu_prevalence, lines =\
preprocess_otu_table(otu_sample_ids, otu_table, lineages,
coords_data, coords_headers, n_taxa_to_keep)
# remove the columns in the mapping file that are not informative taking
# into account the header names that were already authorized to be used
# and take care of concatenating the fields for the && merged columns
mapping_data, header = preprocess_mapping_file(mapping_data, header,
color_by_column_names, unique=not add_unique_columns, clones=clones)
# create the output directory before creating any other output
create_dir(opts.output_dir,False)
fp_out = open(join(output_dir, 'index.html'),'w')
fp_out.write(emperor_autograph+'\n')
fp_out.write(EMPEROR_HEADER_HTML_STRING)
# write the html file
def test_preprocess_otu_table(self):
"""Check the coords and otu table are processed correctly"""
# processing only the four most prevalent taxa
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines =\
preprocess_otu_table(self.otu_sample_ids, self.otu_table,
self.lineages, self.coords, self.coords_header, 4)
assert_almost_equal(
o_otu_coords,
array([[
-6.71083200e-02, 1.05892642e-02, -5.26801821e-03,
-1.31730322e-02, 3.15036935e-02, -1.99712144e-02,
8.14445313e-03, -1.76632227e-02, -4.84141987e-09
],
[
9.65846961e-02, -1.64070839e-02, 1.68610695e-02,
1.03495979e-02, -2.26223522e-02, 2.83763737e-02,
1.76116225e-05, 2.89253284e-02, -4.84141987e-09
],
[
-5.61881305e-04, 1.16341355e-02, -4.97196330e-02,
4.51141625e-02, -1.29353935e-01, -2.14114921e-02,
-6.92988035e-02, -6.27730937e-02, -4.84141987e-09
],
[
-5.70985165e-02, -1.09278921e-02, 8.49830390e-04,
-1.91550282e-02, -4.22122952e-02, 7.75750297e-04,
-1.18543093e-02, 3.31082777e-02, -4.84141987e-09
]]))
assert_almost_equal(
o_otu_table,
array([[
0.78767123, 0.45637584, 0.22, 0.39597315, 0.41610738,
0.20945946, 0.70068027, 0.89932886, 0.77333333
],
[
0.14383562, 0.27516779, 0.65333333, 0.52348993,
0.38926174, 0.69594595, 0.28571429, 0.0738255,
0.19333333
],
[
0.03424658, 0.16107383, 0.02666667, 0.00671141,
0.14765101, 0.01351351, 0., 0.01342282, 0.00666667
],
[
0.02739726, 0.04697987, 0.02, 0.04697987, 0.01,
0.02027027, 0.01360544, 0.01342282, 0.02666667
]]))
self.assertEquals(o_otu_lineages, [
'Root;k__Bacteria;p__Firmicutes',
'Root;k__Bacteria;p__Bacteroidetes',
'Root;k__Bacteria;p__Tenericutes', 'Root;k__Bacteria;Other'
])
assert_almost_equal(o_prevalence,
array([1., 0.66471926, 0.08193196, 0.04374296]))
self.assertEquals(lines, LINES)
# tests for correct outputs of empty inputs
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines =\
preprocess_otu_table([],[], [], self.coords, self.coords_header, 4)
self.assertEquals(o_otu_coords, [])
self.assertEquals(o_otu_table, [])
self.assertEquals(o_otu_lineages, [])
self.assertEquals(o_prevalence, [])
self.assertEquals(lines, '')
def test_preprocess_otu_table(self):
"""Check the coords and otu table are processed correctly"""
# processing only the four most prevalent taxa
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines =\
preprocess_otu_table(self.otu_sample_ids, self.otu_table,
self.lineages, self.coords,
self.coords_header, 4)
assert_almost_equal(o_otu_coords,
array([[-6.71083200e-02, 1.05892642e-02,
-5.26801821e-03, -1.31730322e-02,
3.15036935e-02, -1.99712144e-02,
8.14445313e-03, -1.76632227e-02,
-4.84141987e-09],
[9.65846961e-02, -1.64070839e-02,
1.68610695e-02, 1.03495979e-02,
-2.26223522e-02, 2.83763737e-02,
1.76116225e-05, 2.89253284e-02,
-4.84141987e-09],
[-5.61881305e-04, 1.16341355e-02,
-4.97196330e-02, 4.51141625e-02,
-1.29353935e-01, -2.14114921e-02,
-6.92988035e-02, -6.27730937e-02,
-4.84141987e-09],
[-5.70985165e-02, -1.09278921e-02,
8.49830390e-04, -1.91550282e-02,
-4.22122952e-02, 7.75750297e-04,
-1.18543093e-02, 3.31082777e-02,
-4.84141987e-09]]))
assert_almost_equal(o_otu_table,
array([[0.78767123, 0.45637584, 0.22, 0.39597315,
0.41610738, 0.20945946, 0.70068027,
0.89932886, 0.77333333],
[0.14383562, 0.27516779, 0.65333333,
0.52348993, 0.38926174, 0.69594595,
0.28571429, 0.0738255, 0.19333333],
[0.03424658, 0.16107383, 0.02666667,
0.00671141, 0.14765101, 0.01351351,
0., 0.01342282, 0.00666667],
[0.02739726, 0.04697987, 0.02, 0.04697987,
0.01, 0.02027027, 0.01360544, 0.01342282,
0.02666667]]))
self.assertEquals(o_otu_lineages,
['Root;k__Bacteria;p__Firmicutes',
'Root;k__Bacteria;p__Bacteroidetes',
'Root;k__Bacteria;p__Tenericutes',
'Root;k__Bacteria;Other'])
assert_almost_equal(o_prevalence,
array([1., 0.66471926, 0.08193196, 0.04374296]))
# Avoid string comparisons as reconciling floating point errors there
# would be hard. The function producing this output is already tested
# in tests/test_qiime_backports/test_biplots.py
self.assertEqual(len(lines.split('\n')), 5)
self.assertTrue(lines.startswith('#Taxon\tpc1\tpc2\tpc3\tpc4\tpc5\tpc6'
'\tpc7\tpc8\tpc9\n'))
for lineage in o_otu_lineages:
self.assertTrue(lineage in lines)
# tests for correct outputs of empty inputs
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines =\
preprocess_otu_table([], [], [], self.coords,
self.coords_header, 4)
self.assertEquals(o_otu_coords, [])
self.assertEquals(o_otu_table, [])
self.assertEquals(o_otu_lineages, [])
self.assertEquals(o_prevalence, [])
self.assertEquals(lines, '')
def main():
#option_parser, opts, args = parse_command_line_parameters(**script_info)
input_coords = args.input_coords
map_fp = args.map_fp
output_dir = args.output_dir
color_by_column_names = None #opts.color_by
add_unique_columns = False #opts.add_unique_columns
custom_axes = None #opts.custom_axes
ignore_missing_samples = False #opts.ignore_missing_samples
missing_custom_axes_values = None #opts.missing_custom_axes_values
jackknifing_method = 'IQR' #opts.ellipsoid_method
master_pcoa = None #opts.master_pcoa
taxa_fp = None #opts.taxa_fp
n_taxa_to_keep = False #opts.n_taxa_to_keep
biplot_fp = None #opts.biplot_fp
add_vectors = [None, None] #opts.add_vectors
verbose_output = False #opts.verbose
number_of_axes = 10 #opts.number_of_axes
compare_plots = False #opts.compare_plots
number_of_segments = 8 #opts.number_of_segments
pct_variation_below_one = True #opts.pct_variation_below_one
# add some metadata to the output
emperor_autograph = format_emperor_autograph(map_fp, input_coords, 'HTML')
# verifying that the number of axes requested is greater than 3
if number_of_axes < 3:
print(('You need to plot at least 3 axes.'))
# verifying that the number of segments is between the desired range
if not (4 <= number_of_segments <= 14):
print(('number_of_segments should be between 4 and 14.'))
# append headernames that the script didn't find in the mapping file
# according to different criteria to the following variables
offending_fields = []
non_numeric_categories = []
serial_comparison = True
# can't do averaged pcoa plots _and_ custom axes in the same plot
if custom_axes is not None and isdir(input_coords):
if custom_axes.count(',') > 0:
print(('Jackknifed plots are limited to one custom '
'axis, currently trying to use: %s. Make '
'sure you use only one.' % custom_axes))
# make sure the flag is not misunderstood from the command line interface
if not isdir(input_coords) and compare_plots:
print("Cannot use the '--compare_plots' flag unless the "
"input path is a directory.")
# before creating any output, check correct parsing of the main input files
#try:
mapping_data, header, comments = parse_mapping_file(open(map_fp, 'U'))
try:
pass
except:
sys.exit(("The metadata mapping file '%s' does not seem "
"to be formatted correctly, verify the "
"formatting is QIIME compliant by using "
"validate_mapping_file.py") % map_fp)
else:
# use this set variable to make presence/absensce checks faster
lookup_header = set(header)
mapping_ids = {row[0] for row in mapping_data}
# dir means jackknifing or coordinate comparison type of processing
if isdir(input_coords):
offending_coords_fp = []
coords_headers = []
coords_data = []
coords_eigenvalues = []
coords_pct = []
coord_fps = guess_coordinates_files(input_coords)
# QIIME generates folders of transformed coordinates for the specific
# purpose of connecting all coordinates to a set of origin coordinates.
# The name of this file is suffixed as _transformed_reference.txt
trans_suf = '_transformed_reference.txt'
transformed = [f for f in coord_fps if f.endswith(trans_suf)]
# this could happen and we rather avoid this problem
if len(coord_fps) == 0:
print('Could not use any of the files in the input '
'directory.')
# the master pcoa must be the first in the list of coordinates; however
# if the visualization is not a jackknifed plot this gets ignored
if master_pcoa and not compare_plots:
if master_pcoa in coord_fps: # remove it if duplicated
coord_fps.remove(master_pcoa)
coord_fps = [master_pcoa] + coord_fps # prepend it to the list
# passing a master file means that the comparison is not serial
elif master_pcoa and compare_plots:
serial_comparison = False
# guarantee that the master is the first and is not repeated
if master_pcoa in coord_fps:
coord_fps.remove(master_pcoa)
sorted_filenames = sort_comparison_filenames(coord_fps)
coord_fps = [master_pcoa] + sorted_filenames
elif master_pcoa is None and len(transformed):
master_pcoa = transformed[0]
serial_comparison = False
# Note: the following steps are to guarantee consistency.
# remove the master from the list and re-add it as a first element
# the rest of the files must be sorted alphabetically so the result
# will be: ['unifrac_transformed_reference.txt',
# 'unifrac_transformed_q1.txt', 'unifrac_transformed_q2.txt'] etc
coord_fps.remove(master_pcoa)
coord_fps = [master_pcoa] + sort_comparison_filenames(coord_fps)
for fp in coord_fps:
try:
parsed = parse_coords(open(fp, 'U'))
except (ValueError, QiimeParseError):
offending_coords_fp.append(fp)
# do not add any of the data and move along
continue
else:
# pack all the data correspondingly only if it was correctly
# parsed
coords_headers.append(parsed[0])
coords_data.append(parsed[1])
coords_eigenvalues.append(parsed[2])
coords_pct.append(parsed[3])
# in case there were files that couldn't be parsed
if offending_coords_fp:
errout = ', '.join(offending_coords_fp)
sys.exit(("The following file(s): '%s' could not be "
"parsed properly. Make sure the input folder "
"only contains coordinates files.") % errout)
# check all files contain the same sample identifiers by flattening the
# list of available sample ids and returning the sample ids that are
# in one of the sets of sample ids but not in the globablly shared ids
_coords_headers = set(flatten(coords_headers))
_per_file_missing = [_coords_headers - set(e) for e in coords_headers]
non_shared_ids = set(flatten(_per_file_missing))
if non_shared_ids:
errout = ', '.join(non_shared_ids)
sys.exit(("The following sample identifier(s): '%s' "
"are not shared between all the files. The "
"files used to make a jackknifed PCoA plot "
"or coordinate comparison plot (procustes "
"plot) must share all the same sample "
"identifiers between each other.") % errout)
# number of samples ids that are shared between coords and mapping
# files
sids_intersection = mapping_ids.intersection(_coords_headers)
# sample ids that are not mapped but are in the coords
sids_difference = _coords_headers.difference(mapping_ids)
# used to perform different validations in the script, very similar for
# the case where the input is not a directory
number_intersected_sids = len(sids_intersection)
required_number_of_sids = len(coords_headers[0])
else:
try:
parsed = parse_coords(open(input_coords, 'U'))
# this exception was noticed when there were letters in the coords file
# other exeptions should be catched here; code will be updated then
except (ValueError, QiimeParseError):
sys.exit(("The PCoA file '%s' does not seem to be a "
"coordinates formatted file, verify by "
"manually inspecting the contents.") %
input_coords)
else:
coords_headers = parsed[0]
coords_data = parsed[1]
coords_eigenvalues = parsed[2]
coords_pct = parsed[3]
# number of samples ids that are shared between coords and mapping
# files
sids_intersection = mapping_ids.intersection(coords_headers)
# sample ids that are not mapped but are in the coords
sids_difference = set(coords_headers).difference(mapping_ids)
number_intersected_sids = len(sids_intersection)
required_number_of_sids = len(coords_headers)
if taxa_fp:
try:
# This should really use BIOM's Table.from_tsv
# for summarized tables the "otu_ids" are really the "lineages"
parsed = parse_otu_table(open(taxa_fp, 'U'), count_map_f=float,
remove_empty_rows=True)
except ValueError(e):
sys.exit(("There was a problem parsing the --taxa_fp: "
"%s" % e.message))
else:
otu_sample_ids = parsed[0]
lineages = parsed[1]
otu_table = parsed[2]
# make sure there are matching sample ids with the otu table
if not sids_intersection.issuperset(otu_sample_ids):
sys.exit("The sample identifiers in the OTU table must "
"have at least one match with the data in the "
"mapping file and with the coordinates file. "
"Verify you are using input files that belong "
"to the same dataset.")
if len(lineages) <= 1:
sys.exit("Contingency tables with one or fewer rows "
"are not supported, please try passing a "
"contingency table with more than one row.")
else:
# empty lists indicate that there was no taxa file passed in
otu_sample_ids, lineages, otu_table = [], [], []
# sample ids must be shared between files
if number_intersected_sids <= 0:
sys.exit('None of your sample identifiers match between the'
' mapping file and the coordinates file. Verify '
'you are using a coordinates file and a mapping '
'file that belong to the same dataset.')
# the intersection of the sample ids in the coords and the sample ids in
# the mapping file must at the very least include all ids in the coords
# file Otherwise it isn't valid; unless --ignore_missing_samples is set
# True
if number_intersected_sids != required_number_of_sids:
if ignore_missing_samples:
# keep only the samples that are mapped in the mapping file
coords_headers, coords_data = keep_samples_from_pcoa_data(
coords_headers, coords_data, sids_intersection)
else:
message = ("The metadata mapping file has fewer sample "
"identifiers than the coordinates file. Verify you are "
"using a mapping file that contains at least all the "
"samples contained in the coordinates file(s). You can "
"force the script to ignore these samples by passing "
"the '--ignore_missing_samples' flag.")
if verbose_output:
missing_ids = ', '.join(sids_difference)
message += ' Offending sample identifier(s): %s.' % missing_ids
sys.exit(message)
# ignore samples that exist in the coords but not in the mapping file,
# note: we're using sids_intersection so if --ignore_missing_samples is
# enabled we account for unmapped coords, else the program will exit before
# this point
header, mapping_data = filter_mapping_file(mapping_data, header,
sids_intersection,
include_repeat_cols=True)
# catch the errors that could occur when filling the mapping file values
if missing_custom_axes_values:
# the fact that this uses parse_metadata_state_descriptions makes the
# following option '-x Category:7;PH:12' to work as well as the
# script-interface-documented '-x Category:7 -x PH:12' option
for val in missing_custom_axes_values:
if ':' not in val:
sys.exit("Not valid missing value for custom "
"axes: %s" % val)
_mcav = ';'.join(missing_custom_axes_values)
try:
mapping_data = fill_mapping_field_from_mapping_file(mapping_data,
header, _mcav)
except AssertionError(e):
print(e.message)
except EmperorInputFilesError(e):
print(e.message)
# check that all the required columns exist in the metadata mapping file
if color_by_column_names:
color_by_column_names = color_by_column_names.split(',')
# check for all the mapping fields
for col in color_by_column_names:
# for concatenated columns check each individual field
parts = col.split('&&')
offending_fields.extend(p for p in parts if p not in lookup_header)
else:
# if the user didn't specify the header names display everything
color_by_column_names = [None]
# extract a list of the custom axes provided and each element is numeric
if custom_axes:
custom_axes = custom_axes.strip().strip("'").strip('"').split(',')
# the MetadataMap object makes some checks easier
map_object = MetadataMap(mapping_file_to_dict(mapping_data, header),
[])
for axis in custom_axes:
# append the field to the error queue that it belongs to
if axis not in lookup_header:
offending_fields.append(axis)
break
# make sure this value is in the mapping file
elif axis not in color_by_column_names:
color_by_column_names.append(axis)
# perform only if the for loop does not call break
else:
# make sure all these axes are numeric
for axis in custom_axes:
if not map_object.isNumericCategory(axis):
non_numeric_categories.append(axis)
# make multiple checks for the add_vectors option
if add_vectors != [None, None]:
add_vectors = add_vectors.split(',')
# check there are at the most two categories specified for this option
if len(add_vectors) > 2:
print("The '--add_vectors' option can accept up to "
"two different fields from the mapping file; "
"currently trying to use %d (%s)." %
(len(add_vectors), ', '.join(add_vectors)))
# make sure the field(s) exist
for col in add_vectors:
# concatenated fields are allowed now so check for each field
if '&&' in col:
for _col in col.split('&&'):
if _col not in lookup_header:
offending_fields.append(col)
break
# only execute this block of code if all checked fields exist
else:
# make sure that if it's going to be used for vector
# creation it gets used for coloring and map postprocessing
if col not in color_by_column_names:
color_by_column_names.append(col)
# if it's a column without concatenations
elif col not in lookup_header:
offending_fields.append(col)
break
else:
# check this vector value is in the color by category
if col not in color_by_column_names:
color_by_column_names.append(col)
# perform only if the for loop does not call break
else:
# check that the second category is all with numeric values
if len(add_vectors) == 2:
map_object = MetadataMap(mapping_file_to_dict(mapping_data,
header),
[])
# if it has non-numeric values add it to the list of offenders
if not map_object.isNumericCategory(add_vectors[1]):
msg = add_vectors[1] + '(used in --add_vectors)'
non_numeric_categories.append(msg)
else:
add_vectors.append(None)
# terminate the program for the cases where a mapping field was not found
# or when a mapping field didn't meet the criteria of being numeric
if offending_fields:
sys.exit("Invalid field(s) '%s'; the valid field(s) are: "
"'%s'" % (', '.join(offending_fields),
', '.join(header)))
if non_numeric_categories:
sys.exit(("The following field(s): '%s' contain values "
"that are not numeric, hence not suitable for "
"'--custom_axes' nor for '--add_vectors'. Try "
"the '--missing_custom_axes_values' option to "
"fix these values." %
', '.join(non_numeric_categories)))
# process the coordinates file first, preventing the case where the custom
# axes is not in the coloring categories i. e. in the --colory_by
# categories
preprocessed_coords = preprocess_coords_file(coords_headers, coords_data,
coords_eigenvalues,
coords_pct, header,
mapping_data, custom_axes,
jackknifing_method,
compare_plots,
pct_variation_below_one)
coords_headers = preprocessed_coords[0]
coords_data = preprocessed_coords[1]
coords_eigenvalues = preprocessed_coords[2]
coords_pct = preprocessed_coords[3]
coords_low = preprocessed_coords[4]
coords_high = preprocessed_coords[5]
clones = preprocessed_coords[6]
# process the otu table after processing the coordinates to get custom axes
# (when available) or any other change that occurred to the coordinates
preprocessed_otu_table = preprocess_otu_table(otu_sample_ids, otu_table,
lineages, coords_data,
coords_headers,
n_taxa_to_keep)
otu_coords = preprocessed_otu_table[0]
otu_table = preprocessed_otu_table[1]
otu_lineages = preprocessed_otu_table[2]
otu_prevalence = preprocessed_otu_table[3]
lines = preprocessed_otu_table[4]
# remove the columns in the mapping file that are not informative taking
# into account the header names that were already authorized to be used
# and take care of concatenating the fields for the && merged columns
mapping_data, header = preprocess_mapping_file(mapping_data, header,
color_by_column_names,
not add_unique_columns,
clones=clones)
# create the output directory before creating any other output
if not isdir(opts.output_dir):
makedirs(opts.output_dir)
fp_out = open(join(output_dir, 'index.html'), 'w')
fp_out.write(emperor_autograph+'\n')
fp_out.write(EMPEROR_HEADER_HTML_STRING)
# write the html file
fp_out.write(format_mapping_file_to_js(mapping_data, header, header))
# certain percents being explained cannot be displayed in the GUI
try:
fp_out.write(format_pcoa_to_js(coords_headers, coords_data,
coords_eigenvalues, coords_pct,
custom_axes, coords_low,
coords_high,
number_of_axes=number_of_axes,
number_of_segments=number_of_segments))
except EmperorLogicError(e):
sys.exit(e.message)
fp_out.write(format_taxa_to_js(otu_coords, otu_lineages, otu_prevalence))
fp_out.write(format_vectors_to_js(mapping_data, header, coords_data,
coords_headers, add_vectors[0],
add_vectors[1]))
fp_out.write(format_comparison_bars_to_js(coords_data, coords_headers,
clones, serial_comparison))
has_taxa = taxa_fp is not None
has_input_coords = isdir(input_coords) and not compare_plots
has_add_vectors = add_vectors != [None, None]
has_clones = clones > 0
fp_out.write(format_emperor_html_footer_string(has_taxa, has_input_coords,
has_add_vectors,
has_clones))
fp_out.close()
copy_support_files(output_dir)
# write the biplot coords in the output file if a path is passed
if biplot_fp and taxa_fp:
if biplot_fp.endswith('/') or isdir(biplot_fp):
print("Do not specify a path to a new (path ending "
"in a slash) or existing directory for "
"biplot_fp. The output file will be a "
"tab-delimited text file.")
# make sure this file can be created
try:
fd = open(biplot_fp, 'w')
except IOError:
sys.exit("There was a problem creating the file with "
"the coordinates for the biplots (%s)."
% biplot_fp)
else:
fd.writelines(lines)
fd.close()
def test_preprocess_otu_table(self):
"""Check the coords and otu table are processed correctly"""
# processing only the four most prevalent taxa
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines =\
preprocess_otu_table(self.otu_sample_ids, self.otu_table,
self.lineages, self.coords,
self.coords_header, 4)
assert_almost_equal(
o_otu_coords,
array([[
-6.71083200e-02, 1.05892642e-02, -5.26801821e-03,
-1.31730322e-02, 3.15036935e-02, -1.99712144e-02,
8.14445313e-03, -1.76632227e-02, -4.84141987e-09
],
[
9.65846961e-02, -1.64070839e-02, 1.68610695e-02,
1.03495979e-02, -2.26223522e-02, 2.83763737e-02,
1.76116225e-05, 2.89253284e-02, -4.84141987e-09
],
[
-5.61881305e-04, 1.16341355e-02, -4.97196330e-02,
4.51141625e-02, -1.29353935e-01, -2.14114921e-02,
-6.92988035e-02, -6.27730937e-02, -4.84141987e-09
],
[
-5.70985165e-02, -1.09278921e-02, 8.49830390e-04,
-1.91550282e-02, -4.22122952e-02, 7.75750297e-04,
-1.18543093e-02, 3.31082777e-02, -4.84141987e-09
]]))
assert_almost_equal(
o_otu_table,
array([[
0.78767123, 0.45637584, 0.22, 0.39597315, 0.41610738,
0.20945946, 0.70068027, 0.89932886, 0.77333333
],
[
0.14383562, 0.27516779, 0.65333333, 0.52348993,
0.38926174, 0.69594595, 0.28571429, 0.0738255,
0.19333333
],
[
0.03424658, 0.16107383, 0.02666667, 0.00671141,
0.14765101, 0.01351351, 0., 0.01342282, 0.00666667
],
[
0.02739726, 0.04697987, 0.02, 0.04697987, 0.01,
0.02027027, 0.01360544, 0.01342282, 0.02666667
]]))
self.assertEquals(o_otu_lineages, [
'Root;k__Bacteria;p__Firmicutes',
'Root;k__Bacteria;p__Bacteroidetes',
'Root;k__Bacteria;p__Tenericutes', 'Root;k__Bacteria;Other'
])
assert_almost_equal(o_prevalence,
array([1., 0.66471926, 0.08193196, 0.04374296]))
# Avoid string comparisons as reconciling floating point errors there
# would be hard. The function producing this output is already tested
# in tests/test_qiime_backports/test_biplots.py
self.assertEqual(len(lines.split('\n')), 5)
self.assertTrue(
lines.startswith('#Taxon\tpc1\tpc2\tpc3\tpc4\tpc5\tpc6'
'\tpc7\tpc8\tpc9\n'))
for lineage in o_otu_lineages:
self.assertTrue(lineage in lines)
# tests for correct outputs of empty inputs
o_otu_coords, o_otu_table, o_otu_lineages, o_prevalence, lines =\
preprocess_otu_table([], [], [], self.coords,
self.coords_header, 4)
self.assertEquals(o_otu_coords, [])
self.assertEquals(o_otu_table, [])
self.assertEquals(o_otu_lineages, [])
self.assertEquals(o_prevalence, [])
self.assertEquals(lines, '')
