def setUp(self):
self.data = dict({
"0": "ab",
"1": "abababa",
"2": "abab",
"3": "baba",
"4": "ababaa",
"5": "a",
"6": "abababa",
"7": "bab",
"8": "babba"
})
self.mapping = {
"1": ["0", "2", "5", "6"],
"3": [],
"4": [],
"8": ["7"]
}
self.test_map = {'1': ('a', 'b', 'c'), '2': ('d', 'e', 'f')}
# realistic test file
self.tiny_test = get_qiime_project_dir() +\
"/qiime/support_files/denoiser/TestData/tiny_test.sff.txt"
# set up test file
open("/tmp/denoiser_utils_dummy.tmp", "w")
self.files_to_remove = ["/tmp/denoiser_utils_dummy.tmp"]
self.tmpdir = ""
def setUp(self):
"""define some top-level data"""
qiime_dir = get_qiime_project_dir()
self.key = 'qiime_test'
self.project_id = 'qiime_test'
self.sample_id = 'qiime_sample1'
self.params = [('key', self.key), ('sample', self.sample_id),
('project', self.project_id)]
test_dir = path.dirname(path.abspath(__file__))
self.seq_file = path.join(test_dir, 'test_support_files',
'qiime_tutorial_split_lib_seqs_subset.fna')
self.output_dir = mkdtemp()
self.sample_file = [('file', 'qiime_test.fna', fasta_example)]
self._paths_to_clean_up = []
self._dirs_to_clean_up = []
# make the webfile directory
try:
mkdir(self.output_dir)
except OSError:
pass
# define directory to clean up
self._dirs_to_clean_up = [self.output_dir]
def setUp(self):
self.test_map = {'1': ('a', 'b', 'c'),
'2': ('d', 'e', 'f')}
self.labels = [
'Uneven1_1 FV9NWLF.01.EVGI8 orig_bc=TCGAGCGAATCT new_bc=TCGAGCGAATCT bc_diffs=0',
'Even1_2 FV9NWLF.01.DROG9 orig_bc=TAGTTGCGAGTC new_bc=TAGTTGCGAGTC bc_diffs=0',
'Uneven1_3 FV9NWLF.01.DZTVJ orig_bc=TCGAGCGAATCT new_bc=TCGAGCGAATCT bc_diffs=0',
'Uneven3_4 FV9NWLF.01.DI8SC orig_bc=TCTGCTAGATGT new_bc=TCTGCTAGATGT bc_diffs=0',
'Even3_5 FV9NWLF.01.DW381 orig_bc=TCATCGCGATAT new_bc=TCATCGCGATAT bc_diffs=0',
'Even3_6 FV9NWLF01DP96S orig_bc=TCATCGCGATAT new_bc=TCATCGCGATAT bc_diffs=0',
'Uneven2_7 FV9NWLF01BOY7E orig_bc=TCGTTCACATGA new_bc=TCGTTCACATGA bc_diffs=0',
'Even1_8 FV9NWLF01A0OG1 orig_bc=TAGTTGCGAGTC new_bc=TAGTTGCGAGTC bc_diffs=0',
'Even2_9 FV9NWLF01DJZFF orig_bc=TCACGATTAGCG new_bc=TCACGATTAGCG bc_diffs=0',
'Uneven1_10 FV9NWLF01D4LTB orig_bc=TCGAGCGAATCT new_bc=TCGAGCGAATCT bc_diffs=0']
self.invalid_sequence_identifiers = [
['Uneven1_1 FV9NWLF_01_EVGI8 orig_bc=TCGAGCGAATCT new_bc=TCGAGCGAATCT bc_diffs=0'],
['Even1_2 FV9NWLF_01_DROG9 orig_bc=TAGTTGCGAGTC new_bc=TAGTTGCGAGTC bc_diffs=0'],
['Even1_8 FV9NWLF-01-A0OG1 orig_bc=TAGTTGCGAGTC new_bc=TAGTTGCGAGTC bc_diffs=0'],
['Even2_9 FV9NWLF_01-DJZFF orig_bc=TCACGATTAGCG new_bc=TCACGATTAGCG bc_diffs=0'],
['Uneven1_10 FV9NWLF_01.D4LTB orig_bc=TCGAGCGAATCT new_bc=TCGAGCGAATCT bc_diffs=0']]
self.tiny_test = get_qiime_project_dir() +\
"/qiime/support_files/denoiser/TestData/tiny_test.sff.txt"
def setUp(self):
"""define some top-level data"""
qiime_dir = get_qiime_project_dir()
self.key = 'qiime_test'
self.project_id = 'qiime_test'
self.sample_id = 'qiime_sample1'
self.params=[('key', self.key), ('sample', self.sample_id), \
('project', self.project_id)]
test_dir = path.dirname(path.abspath(__file__))
self.seq_file=path.join(test_dir,'test_support_files',\
'qiime_tutorial_split_lib_seqs_subset.fna')
self.output_dir = get_random_directory_name(output_dir='/tmp/')
self.sample_file = [('file', 'qiime_test.fna', fasta_example)]
self._paths_to_clean_up = []
self._dirs_to_clean_up = []
#make the webfile directory
try:
mkdir(self.output_dir)
except OSError:
pass
#define directory to clean up
self._dirs_to_clean_up = [self.output_dir]
def test_for_obsolete_values(self):
"""local qiime_config has no extra params"""
qiime_project_dir = get_qiime_project_dir()
orig_config = parse_qiime_config_file(open(qiime_project_dir +
'/qiime/support_files/qiime_config'))
#check the env qiime_config
qiime_config_env_filepath = getenv('QIIME_CONFIG_FP')
if qiime_config_env_filepath:
qiime_config_via_env= parse_qiime_config_file(open(qiime_config_env_filepath))
extra_vals = []
for key in qiime_config_via_env:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The qiime_config file set via QIIME_CONFIG_FP"+
"enviroment variable contains obsolete parameters:\n"+
", ".join(extra_vals))
# check the qiime_config in $HOME/.qiime_config
home_dir = getenv('HOME')
if (exists(home_dir+"/.qiime_config")):
qiime_config_home = parse_qiime_config_file(open(home_dir+"/.qiime_config"))
extra_vals = []
for key in qiime_config_home:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The .qiime_config in your HOME contains obsolete "+
"parameters:\n" + ", ".join(extra_vals))
def test_for_obsolete_values(self):
"""local qiime_config has no extra params"""
qiime_project_dir = get_qiime_project_dir()
orig_config = parse_qiime_config_file(open(qiime_project_dir +
'/qiime/support_files/qiime_config'))
#check the env qiime_config
qiime_config_env_filepath = getenv('QIIME_CONFIG_FP')
if qiime_config_env_filepath:
qiime_config_via_env= parse_qiime_config_file(open(qiime_config_env_filepath))
extra_vals = []
for key in qiime_config_via_env:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The qiime_config file set via QIIME_CONFIG_FP"+
"enviroment variable contains obsolete parameters:\n"+
", ".join(extra_vals))
# check the qiime_config in $HOME/.qiime_config
home_dir = getenv('HOME')
if (exists(home_dir+"/.qiime_config")):
qiime_config_home = parse_qiime_config_file(open(home_dir+"/.qiime_config"))
extra_vals = []
for key in qiime_config_home:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The .qiime_config in your HOME contains obsolete "+
"parameters:\n" + ", ".join(extra_vals))
def setUp(self):
self.test_map = {"1": ("a", "b", "c"), "2": ("d", "e", "f")}
self.labels = [
"Uneven1_1 FV9NWLF.01.EVGI8 orig_bc=TCGAGCGAATCT new_bc=TCGAGCGAATCT bc_diffs=0",
"Even1_2 FV9NWLF.01.DROG9 orig_bc=TAGTTGCGAGTC new_bc=TAGTTGCGAGTC bc_diffs=0",
"Uneven1_3 FV9NWLF.01.DZTVJ orig_bc=TCGAGCGAATCT new_bc=TCGAGCGAATCT bc_diffs=0",
"Uneven3_4 FV9NWLF.01.DI8SC orig_bc=TCTGCTAGATGT new_bc=TCTGCTAGATGT bc_diffs=0",
"Even3_5 FV9NWLF.01.DW381 orig_bc=TCATCGCGATAT new_bc=TCATCGCGATAT bc_diffs=0",
"Even3_6 FV9NWLF01DP96S orig_bc=TCATCGCGATAT new_bc=TCATCGCGATAT bc_diffs=0",
"Uneven2_7 FV9NWLF01BOY7E orig_bc=TCGTTCACATGA new_bc=TCGTTCACATGA bc_diffs=0",
"Even1_8 FV9NWLF01A0OG1 orig_bc=TAGTTGCGAGTC new_bc=TAGTTGCGAGTC bc_diffs=0",
"Even2_9 FV9NWLF01DJZFF orig_bc=TCACGATTAGCG new_bc=TCACGATTAGCG bc_diffs=0",
"Uneven1_10 FV9NWLF01D4LTB orig_bc=TCGAGCGAATCT new_bc=TCGAGCGAATCT bc_diffs=0",
]
self.invalid_sequence_identifiers = [
["Uneven1_1 FV9NWLF_01_EVGI8 orig_bc=TCGAGCGAATCT new_bc=TCGAGCGAATCT bc_diffs=0"],
["Even1_2 FV9NWLF_01_DROG9 orig_bc=TAGTTGCGAGTC new_bc=TAGTTGCGAGTC bc_diffs=0"],
["Even1_8 FV9NWLF-01-A0OG1 orig_bc=TAGTTGCGAGTC new_bc=TAGTTGCGAGTC bc_diffs=0"],
["Even2_9 FV9NWLF_01-DJZFF orig_bc=TCACGATTAGCG new_bc=TCACGATTAGCG bc_diffs=0"],
["Uneven1_10 FV9NWLF_01.D4LTB orig_bc=TCGAGCGAATCT new_bc=TCGAGCGAATCT bc_diffs=0"],
]
self.tiny_test = get_qiime_project_dir() + "/qiime/support_files/denoiser/TestData/tiny_test.sff.txt"
def test_for_unrecognized_values(self):
"""qiime_config has no extra values"""
error_msg_fragment = (" contains unrecognized values:\n%s\nYou can "
"safely remove these values from your QIIME "
"config file as they will be ignored by QIIME.")
qiime_project_dir = get_qiime_project_dir()
orig_config = parse_qiime_config_file(
open(qiime_project_dir + '/qiime/support_files/qiime_config'))
# check the env qiime_config
qiime_config_env_filepath = getenv('QIIME_CONFIG_FP')
if qiime_config_env_filepath:
qiime_config_via_env = parse_qiime_config_file(
open(qiime_config_env_filepath))
extra_vals = []
for key in qiime_config_via_env:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The QIIME config file set via the QIIME_CONFIG_FP "
"environment variable" +
error_msg_fragment % ", ".join(extra_vals))
# check the qiime_config in $HOME/.qiime_config
home_dir = getenv('HOME')
if (exists(home_dir + "/.qiime_config")):
qiime_config_home = parse_qiime_config_file(
open(home_dir + "/.qiime_config"))
extra_vals = []
for key in qiime_config_home:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The .qiime_config in your HOME" +
error_msg_fragment % ", ".join(extra_vals))
def test_for_unrecognized_values(self):
"""qiime_config has no extra values"""
error_msg_fragment = (" contains unrecognized values:\n%s\nYou can "
"safely remove these values from your QIIME "
"config file as they will be ignored by QIIME.")
qiime_project_dir = get_qiime_project_dir()
orig_config = parse_qiime_config_file(open(qiime_project_dir +
'/qiime/support_files/qiime_config'))
# check the env qiime_config
qiime_config_env_filepath = getenv('QIIME_CONFIG_FP')
if qiime_config_env_filepath:
qiime_config_via_env = parse_qiime_config_file(
open(qiime_config_env_filepath))
extra_vals = []
for key in qiime_config_via_env:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The QIIME config file set via the QIIME_CONFIG_FP "
"environment variable" +
error_msg_fragment % ", ".join(extra_vals))
# check the qiime_config in $HOME/.qiime_config
home_dir = getenv('HOME')
if (exists(home_dir + "/.qiime_config")):
qiime_config_home = parse_qiime_config_file(
open(home_dir + "/.qiime_config"))
extra_vals = []
for key in qiime_config_home:
if key not in orig_config:
extra_vals.append(key)
if extra_vals:
self.fail("The .qiime_config in your HOME" +
error_msg_fragment % ", ".join(extra_vals))
def test_support_files_available(self):
"""support_files are available """
# check that the qiime/support_files directory exists
support_files_dir = \
join(get_qiime_project_dir(),'qiime','support_files')
self.assertTrue(exists(support_files_dir))
# check that a file in qiime/support_files exists
default_qiime_config_fp = join(support_files_dir,'qiime_config')
self.assertTrue(exists(default_qiime_config_fp))
def test_support_files_available(self):
"""support_files are available """
# check that the qiime/support_files directory exists
support_files_dir = \
join(get_qiime_project_dir(),'qiime','support_files')
self.assertTrue(exists(support_files_dir))
# check that a file in qiime/support_files exists
default_qiime_config_fp = join(support_files_dir, 'qiime_config')
self.assertTrue(exists(default_qiime_config_fp))
def test_generate_heatmap_plots(self):
"""generate_heatmap_plots: create default output files"""
# create directories and move js files to verify everything works
# in the script file
dir_path = join(self.output_dir, 'test')
create_dir(dir_path)
js_dir_path = join(dir_path, 'js')
create_dir(js_dir_path)
self._folders_to_cleanup.append(dir_path)
qiime_dir = get_qiime_project_dir()
js_path = join(qiime_dir, 'qiime/support_files/js')
shutil.copyfile(join(js_path, 'overlib.js'),
join(js_dir_path, 'overlib.js'))
shutil.copyfile(join(js_path, 'otu_count_display.js'),
join(js_dir_path, 'otu_count_display.js'))
shutil.copyfile(join(js_path, 'jquery.js'),
join(js_dir_path, 'jquery.js'))
shutil.copyfile(join(js_path, 'jquery.tablednd_0_5.js'),
join(js_dir_path, 'jquery.tablednd_0_5.js'))
# generate otu_table object
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"]
}])
# put in an OTU sort order and sample order
otu_sort = ['OTU2', 'OTU1']
sample_sort = ['Sample2', 'Sample1', 'Sample3']
num_otu_hits = 3
# generate test files
generate_heatmap_plots(num_otu_hits,
orig_otu_table,
otu_sort,
sample_sort,
dir_path,
js_dir_path,
'test',
fractional_values=False)
self.assertEqual(
open(join(js_dir_path, 'test.js'), 'U').read(), exp_js_output_file)
def test_generate_heatmap_plots(self):
"""generate_heatmap_plots: create default output files"""
# create directories and move js files to verify everything works
# in the script file
dir_path = join(self.output_dir, 'test')
create_dir(dir_path)
js_dir_path = join(dir_path, 'js')
create_dir(js_dir_path)
self._folders_to_cleanup.append(dir_path)
qiime_dir = get_qiime_project_dir()
js_path = join(qiime_dir, 'qiime/support_files/js')
shutil.copyfile(join(js_path, 'overlib.js'),
join(js_dir_path, 'overlib.js'))
shutil.copyfile(join(js_path, 'otu_count_display.js'),
join(js_dir_path, 'otu_count_display.js'))
shutil.copyfile(join(js_path, 'jquery.js'),
join(js_dir_path, 'jquery.js'))
shutil.copyfile(join(js_path, 'jquery.tablednd_0_5.js'),
join(js_dir_path, 'jquery.tablednd_0_5.js'))
# generate otu_table object
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"]}])
# put in an OTU sort order and sample order
otu_sort = ['OTU2', 'OTU1']
sample_sort = ['Sample2', 'Sample1', 'Sample3']
num_otu_hits = 3
# generate test files
generate_heatmap_plots(num_otu_hits, orig_otu_table, otu_sort,
sample_sort, dir_path, js_dir_path,
'test', fractional_values=False)
self.assertEqual(open(join(js_dir_path, 'test.js'), 'U').read(),
exp_js_output_file)
def setUp(self):
self.data = dict({"0": "ab", "1":"abababa", "2":"abab",
"3":"baba", "4":"ababaa","5":"a", "6":"abababa",
"7":"bab", "8":"babba"})
self.mapping = {"1":["0","2","5","6"],
"3":[],
"4":[],
"8":["7"]}
self.test_map = {'1': ('a','b','c'),
'2': ('d','e','f')}
#realistic test file
self.tiny_test = get_qiime_project_dir() +\
"/qiime/support_files/denoiser/TestData/tiny_test.sff.txt"
#set up test file
open("/tmp/denoiser_utils_dummy.tmp","w")
self.files_to_remove=["/tmp/denoiser_utils_dummy.tmp"]
self.tmpdir=""
def test_get_qiime_project_dir(self):
"""getting the qiime project directory functions as expected """
# Do an explicit check on whether the file system containing
# the current file is case insensitive. This is in response
# to SF bug #2945548, where this test would fail on certain
# unusual circumstances on case-insensitive file systems
# because the case of abspath(__file__) was inconsistent.
# (If you don't believe this, set case_insensitive_filesystem
# to False, and rename your top-level Qiime directory as
# qiime on OS X. That sould cause this test to fail as
# actual will be path/to/qiime and expected will be
# path/to/Qiime.) Note that we don't need to change anything
# in the get_qiime_project_dir() function as if the
# file system is case insenstive, the case of the returned
# string is irrelevant.
case_insensitive_filesystem = \
exists(__file__.upper()) and exists(__file__.lower())
actual = get_qiime_project_dir()
# I base the expected here off the imported location of
# qiime/util.py here, to handle cases where either the user has
# Qiime in their PYTHONPATH, or when they've installed it with
# setup.py.
# If util.py moves this test will fail -- that
# is what we want in this case, as the get_qiime_project_dir()
# function would need to be modified.
import qiime.util
util_py_filepath = abspath(abspath(qiime.util.__file__))
expected = dirname(dirname(util_py_filepath))
if case_insensitive_filesystem:
# make both lowercase if the file system is case insensitive
actual = actual.lower()
expected = expected.lower()
self.assertEqual(actual,expected)
def test_get_qiime_project_dir(self):
"""getting the qiime project directory functions as expected """
# Do an explicit check on whether the file system containing
# the current file is case insensitive. This is in response
# to SF bug #2945548, where this test would fail on certain
# unusual circumstances on case-insensitive file systems
# because the case of abspath(__file__) was inconsistent.
# (If you don't believe this, set case_insensitive_filesystem
# to False, and rename your top-level Qiime directory as
# qiime on OS X. That sould cause this test to fail as
# actual will be path/to/qiime and expected will be
# path/to/Qiime.) Note that we don't need to change anything
# in the get_qiime_project_dir() function as if the
# file system is case insenstive, the case of the returned
# string is irrelevant.
case_insensitive_filesystem = \
exists(__file__.upper()) and exists(__file__.lower())
actual = get_qiime_project_dir()
# I base the expected here off the imported location of
# qiime/util.py here, to handle cases where either the user has
# Qiime in their PYTHONPATH, or when they've installed it with
# setup.py.
# If util.py moves this test will fail -- that
# is what we want in this case, as the get_qiime_project_dir()
# function would need to be modified.
import qiime.util
util_py_filepath = abspath(abspath(qiime.util.__file__))
expected = dirname(dirname(util_py_filepath))
if case_insensitive_filesystem:
# make both lowercase if the file system is case insensitive
actual = actual.lower()
expected = expected.lower()
self.assertEqual(actual, expected)
def setUp(self):
"""define some top-level data"""
qiime_dir = get_qiime_project_dir()
self.key = "qiime_test"
self.project_id = "qiime_test"
self.sample_id = "qiime_sample1"
self.params = [("key", self.key), ("sample", self.sample_id), ("project", self.project_id)]
test_dir = path.dirname(path.abspath(__file__))
self.seq_file = path.join(test_dir, "test_support_files", "qiime_tutorial_split_lib_seqs_subset.fna")
self.output_dir = get_random_directory_name(output_dir="/tmp/")
self.sample_file = [("file", "qiime_test.fna", fasta_example)]
self._paths_to_clean_up = []
self._dirs_to_clean_up = []
# make the webfile directory
try:
mkdir(self.output_dir)
except OSError:
pass
# define directory to clean up
self._dirs_to_clean_up = [self.output_dir]
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
prefs, data, background_color, label_color, ball_scale, arrow_colors = \
sample_color_prefs_and_map_data_from_options(opts)
if len(opts.coord_fnames) < 2 and opts.edges_file is None:
option_parser.error('Please provide at least two ' +\
'coordinate files or a custom edges file')
#Open and get coord data (for multiple coords files)
coord_files = opts.coord_fnames
coord_files_valid = validate_coord_files(coord_files)
if not coord_files_valid:
option_parser.error('Every line of every coord file must ' +\
'have the same number of columns.')
num_coord_files = len(coord_files)
data['edges'], data['coord'] = \
get_multiple_coords(coord_files, opts.edges_file, opts.serial)
# if the edges file wasn't supplied, we appended _i to each file's samples
# therefore we now add duplicated samples with _0, _1,... to mapping file
if opts.edges_file is None:
newmap = [data['map'][0]]
for i in xrange(len(coord_files)):
for sample in data['map'][1:]:
newsample = ['%s_%d' %(sample[0],i)]
newsample.extend(sample[1:])
newmap.append(newsample)
data['map'] = newmap
# remove any samples not present in mapping file
remove_unmapped_samples(data['map'],data['coord'],data['edges'])
if(len(data['coord'][1]) == 0):
raise ValueError, '\n\nError: None of the sample IDs in the coordinates files were present in the mapping file.\n'
# process custom axes, if present.
custom_axes = None
if opts.custom_axes:
custom_axes = process_custom_axes(opts.custom_axes)
get_custom_coords(custom_axes, data['map'], data['coord'])
remove_nans(data['coord'])
scale_custom_coords(custom_axes,data['coord'])
# Generate random output file name and create directories
if opts.output_dir:
create_dir(opts.output_dir)
dir_path = opts.output_dir
else:
dir_path='./'
qiime_dir=get_qiime_project_dir()
jar_path=os.path.join(qiime_dir,'qiime/support_files/jar/')
data_dir_path = get_random_directory_name(output_dir=dir_path,
return_absolute_path=False)
try:
os.mkdir(data_dir_path)
except OSError:
pass
jar_dir_path = os.path.join(dir_path,'jar')
try:
os.mkdir(jar_dir_path)
except OSError:
pass
shutil.copyfile(os.path.join(jar_path,'king.jar'), os.path.join(jar_dir_path,'king.jar'))
filepath=coord_files[0]
filename=filepath.strip().split('/')[-1]
try:
action = generate_3d_plots
except NameError:
action = None
#Place this outside try/except so we don't mask NameError in action
if action:
generate_3d_plots(prefs, data, custom_axes,
background_color, label_color,
dir_path, data_dir_path, filename,
ball_scale=ball_scale, arrow_colors=arrow_colors,
user_supplied_edges=not(opts.edges_file is None))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
matplotlib_version = re.split("[^\d]", matplotlib.__version__)
matplotlib_version_info = tuple([int(i) for i in matplotlib_version if \
i.isdigit()])
if matplotlib_version_info != (1,1,0):
print "This code was only tested with Matplotlib-1.1.0"
data = {}
prefs,data,background_color,label_color,ball_scale, arrow_colors= \
sample_color_prefs_and_map_data_from_options(opts)
data['ellipsoid_method']=opts.ellipsoid_method
if 0.00 <= opts.ellipsoid_opacity <= 1.00:
data['alpha']=opts.ellipsoid_opacity
else:
raise ValueError, 'The opacity must be a value between 0 and 1!'
#Open and get coord data
if os.path.isdir(opts.coord_fname) and opts.master_pcoa:
data['coord'],data['support_pcoas'] = load_pcoa_files(opts.coord_fname)
data['coord']=get_coord(opts.master_pcoa)
elif os.path.isdir(opts.coord_fname):
data['coord'],data['support_pcoas'] = load_pcoa_files(opts.coord_fname)
else:
data['coord'] = get_coord(opts.coord_fname)
filepath=opts.coord_fname
basename,extension=os.path.splitext(filepath)
filename='%s_2D_PCoA_plots' % (basename)
qiime_dir=get_qiime_project_dir()
js_path=os.path.join(qiime_dir,'qiime','support_files','js')
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='./'
html_dir_path=dir_path
data_dir_path = get_random_directory_name(output_dir=dir_path)
try:
os.mkdir(data_dir_path)
except OSError:
pass
js_dir_path = os.path.join(html_dir_path,'js')
try:
os.mkdir(js_dir_path)
except OSError:
pass
shutil.copyfile(os.path.join(js_path,'overlib.js'), \
os.path.join(js_dir_path,'overlib.js'))
try:
action = generate_2d_plots
except NameError:
action = None
#Place this outside try/except so we don't mask NameError in action
if action:
action(prefs,data,html_dir_path,data_dir_path,filename,background_color,
label_color,opts.scree)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# get QIIME directory
qiime_dir = get_qiime_project_dir()
if not opts.counts_fname:
option_parser.error("A list of input files must be specified")
# get color preferences
color_prefs, color_data, background_color, label_color = taxonomy_color_prefs_and_map_data_from_options(opts)
colorby = opts.colorby
if colorby == None:
colorby = []
for c in color_data["counts"].values():
colorby.extend(c[0])
else:
colorby = colorby.strip().strip("'").split(",")
counts_fname = opts.counts_fname
# Define labels to use
labels = opts.labels
if not opts.labels:
new_labels = []
# create an empty list since the user didn't specify labels
for i in counts_fname:
new_labels.append("")
labels = ",".join(new_labels)
data = [(label, f.strip()) for f, label in zip(counts_fname, labels.split(","))]
filepath = data[0][1]
filename = filepath.strip().rpartition("/")[0]
num_categories = int(opts.num_categories)
if num_categories <= 0:
raise ValueError, "The number of categories has to be greater than 0!"
# create directory path
dir_path = os.getcwd()
if opts.dir_path:
dir_path = opts.dir_path
try:
create_dir(opts.dir_path)
except OSError:
pass
# make javascript output directory
javascript_path = os.path.join(dir_path, "js")
try:
create_dir(javascript_path)
except OSError: # raised if dir exists
pass
# make raw_data output directory
raw_data_path = os.path.join(dir_path, "raw_data")
try:
create_dir(raw_data_path)
except OSError: # raised if dir exists
pass
# move javascript file to javascript output directory
shutil.copyfile(
os.path.join(qiime_dir, "qiime", "support_files", "js/overlib.js"), os.path.join(javascript_path, "overlib.js")
)
# make css output directory
css_path = os.path.join(dir_path, "css")
try:
create_dir(css_path)
except OSError: # raised if dir exists
pass
# move css file to css output directory
shutil.copyfile(
os.path.join(qiime_dir, "qiime", "support_files", "css/qiime_style.css"),
os.path.join(css_path, "qiime_style.css"),
)
# verify all parameters are valid
plot_width = float(opts.x_width)
if plot_width <= 0:
raise ValueError, "The width of the plot has to be greater than 0!"
plot_height = float(opts.y_height)
if plot_height <= 0:
raise ValueError, "The height of the plot has to be greater than 0!"
bar_width = float(opts.bar_width)
if bar_width <= 0 or bar_width > 1:
raise ValueError, "The bar width of the plot has to be between 0 and 1!"
dpi = float(opts.dpi)
if dpi <= 0:
raise ValueError, "The dpi of the plot has to be greater than 0!"
resize_nth_label = int(opts.resize_nth_label)
if resize_nth_label < 0:
raise ValueError, "The resize_nth_label of the plot has to be greater\
than 0!"
generate_image_type = opts.type_of_file
label_type = opts.label_type
include_html_legend = opts.include_html_legend
include_html_counts = opts.include_html_counts
plots_to_make = opts.chart_type
for chart_type in plots_to_make:
# make pie chart output path
charts_path = os.path.join(dir_path, "charts")
try:
create_dir(charts_path)
except OSError: # raised if dir exists
pass
make_all_charts(
data,
dir_path,
filename,
num_categories,
colorby,
args,
color_data,
color_prefs,
background_color,
label_color,
chart_type,
generate_image_type,
plot_width,
plot_height,
bar_width,
dpi,
resize_nth_label,
label_type,
include_html_legend,
include_html_counts,
)
def get_denoiser_data_dir():
"""Return the directory of the denoiser error profiles.
"""
dir = get_qiime_project_dir() + "/qiime/support_files/denoiser/Data/"
return dir
def main():
print "\nWarning: make_3d_plots.py is being deprecated in favor of make_emperor.py, and will no longer be available in QIIME 1.8.0-dev.\n"
option_parser, opts, args = parse_command_line_parameters(**script_info)
prefs, data, background_color, label_color, ball_scale, arrow_colors= \
sample_color_prefs_and_map_data_from_options(opts)
plot_scaled= 'scaled' in opts.scaling_method
plot_unscaled= 'unscaled' in opts.scaling_method
if opts.output_format == 'invue':
# validating the number of points for interpolation
if (opts.interpolation_points<0):
option_parser.error('The --interpolation_points should be ' +\
'greater or equal to 0.')
# make sure that coord file has internally consistent # of columns
coord_files_valid = validate_coord_files(opts.coord_fname)
if not coord_files_valid:
option_parser.error('Every line of every coord file must ' +\
'have the same number of columns.')
#Open and get coord data
data['coord'] = get_coord(opts.coord_fname, opts.ellipsoid_method)
# remove any samples not present in mapping file
remove_unmapped_samples(data['map'],data['coord'])
# if no samples overlapped between mapping file and otu table, exit
if len(data['coord'][0]) == 0:
print "\nError: OTU table and mapping file had no samples in common\n"
exit(1)
if opts.output_dir:
create_dir(opts.output_dir,False)
dir_path=opts.output_dir
else:
dir_path='./'
filepath=opts.coord_fname
if os.path.isdir(filepath):
coord_files = [fname for fname in os.listdir(filepath) if not \
fname.startswith('.')]
filename = os.path.split(coord_files[0])[-1]
else:
filename = os.path.split(filepath)[-1]
generate_3d_plots_invue(prefs, data, dir_path, filename, \
opts.interpolation_points, opts.polyhedron_points, \
opts.polyhedron_offset)
#finish script
return
# Potential conflicts
if not opts.custom_axes is None and os.path.isdir(opts.coord_fname):
# can't do averaged pcoa plots _and_ custom axes in the same plot
option_parser.error("Please supply either custom axes or multiple coordinate \
files, but not both.")
# check that smoothness is an integer between 0 and 3
try:
ellipsoid_smoothness = int(opts.ellipsoid_smoothness)
except:
option_parser.error("Please supply an integer ellipsoid smoothness \
value.")
if ellipsoid_smoothness < 0 or ellipsoid_smoothness > 3:
option_parser.error("Please supply an ellipsoid smoothness value \
between 0 and 3.")
# check that opacity is a float between 0 and 1
try:
ellipsoid_alpha = float(opts.ellipsoid_opacity)
except:
option_parser.error("Please supply a number for ellipsoid opacity.")
if ellipsoid_alpha < 0 or ellipsoid_alpha > 1:
option_parser.error("Please supply an ellipsoid opacity value \
between 0 and 1.")
# check that ellipsoid method is valid
ellipsoid_methods = ['IQR','sdev']
if not opts.ellipsoid_method in ellipsoid_methods:
option_parser.error("Please supply a valid ellipsoid method. \
Valid methods are: " + ', '.join(ellipsoid_methods) + ".")
# gather ellipsoid drawing preferences
ellipsoid_prefs = {}
ellipsoid_prefs["smoothness"] = ellipsoid_smoothness
ellipsoid_prefs["alpha"] = ellipsoid_alpha
# make sure that coord file has internally consistent # of columns
coord_files_valid = validate_coord_files(opts.coord_fname)
if not coord_files_valid:
option_parser.error('Every line of every coord file must ' +\
'have the same number of columns.')
#Open and get coord data
data['coord'] = get_coord(opts.coord_fname, opts.ellipsoid_method)
# remove any samples not present in mapping file
remove_unmapped_samples(data['map'],data['coord'])
# if no samples overlapped between mapping file and otu table, exit
if len(data['coord'][0]) == 0:
print "\nError: OTU table and mapping file had no samples in common\n"
exit(1)
# process custom axes, if present.
custom_axes = None
if opts.custom_axes:
custom_axes = process_custom_axes(opts.custom_axes)
get_custom_coords(custom_axes, data['map'], data['coord'])
remove_nans(data['coord'])
scale_custom_coords(custom_axes,data['coord'])
# process vectors if requested
if opts.add_vectors:
add_vectors={}
add_vectors['vectors'] = opts.add_vectors.split(',')
add_vectors['weight_by_vector'] = opts.weight_by_vector
if len(add_vectors)>3:
raise ValueError, 'You must add maximum 3 columns but %s' % opts.add_vectors
# Validating Vectors values
if opts.vectors_algorithm:
axes_number = len(data['coord'][1][1])
if opts.vectors_axes<0 or opts.vectors_axes>axes_number:
raise ValueError, 'vectors_algorithm should be between 0 and the max number' +\
'of samples/pcoa-axes: %d' % len(data['coord'][1][1])
if opts.vectors_axes == 0:
opts.vectors_axes = axes_number
add_vectors['vectors_axes'] = opts.vectors_axes
valid_chars = '_.abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789'
for c in opts.vectors_path:
if c not in valid_chars:
raise ValueError, 'vectors_path (%s) has invalid chars' % opts.vectors_path
add_vectors['vectors_output'] = {}
add_vectors['vectors_algorithm']=opts.vectors_algorithm
add_vectors['eigvals'] = data['coord'][3]
add_vectors['window_size'] = None
# checks specific for the modified first difference algorithm
if add_vectors['vectors_algorithm'] == 'wdiff':
try:
add_vectors['window_size'] = int(opts.window_size)
except TypeError:
raise TypeError, 'Specify --window_size as an integer'
# sanity check as the value can only be greater or equal to one
if add_vectors['window_size'] < 1:
raise ValueError, 'The value of window_size is invalid, '+\
'the value must be greater than zero, not %d' % add_vectors['window_size']
else:
add_vectors['vectors_algorithm'] = None
add_vectors['vectors_path'] = opts.vectors_path
else:
add_vectors = None
if opts.taxa_fname != None:
# get taxonomy counts
# get list of sample_ids that haven't been removed
sample_ids = data['coord'][0]
# get taxa summaries for all sample_ids
lineages, taxa_counts = get_taxa(opts.taxa_fname, sample_ids)
data['taxa'] = {}
data['taxa']['lineages'] = lineages
data['taxa']['counts'] = taxa_counts
# get average relative abundance of taxa
data['taxa']['prevalence'] = get_taxa_prevalence(data['taxa']['counts'])
# get coordinates of taxa (weighted mean of sample scores)
data['taxa']['coord'] = get_taxa_coords(data['taxa']['counts'],
data['coord'][1])
# trim results, do NOT change order
# check: https://github.com/qiime/qiime/issues/677
remove_rare_taxa(data['taxa'],nkeep=opts.n_taxa_keep)
# write taxa coords if requested
if not opts.biplot_output_file is None:
output = make_biplot_scores_output(data['taxa'])
fout = open(opts.biplot_output_file,'w')
fout.write('\n'.join(output))
fout.close()
if opts.output_dir:
create_dir(opts.output_dir,False)
dir_path=opts.output_dir
else:
dir_path='./'
qiime_dir=get_qiime_project_dir()
jar_path=os.path.join(qiime_dir,'qiime/support_files/jar/')
data_dir_path = get_random_directory_name(output_dir=dir_path,
return_absolute_path=False)
try:
os.mkdir(data_dir_path)
except OSError:
pass
data_file_path=data_dir_path
jar_dir_path = os.path.join(dir_path,'jar')
try:
os.mkdir(jar_dir_path)
except OSError:
pass
shutil.copyfile(os.path.join(jar_path,'king.jar'), os.path.join(jar_dir_path,'king.jar'))
filepath=opts.coord_fname
if os.path.isdir(filepath):
coord_files = [fname for fname in os.listdir(filepath) if not \
fname.startswith('.')]
filename = os.path.split(coord_files[0])[-1]
else:
filename = os.path.split(filepath)[-1]
try:
action = generate_3d_plots
except NameError:
action = None
#Place this outside try/except so we don't mask NameError in action
if action:
action(prefs,data,custom_axes,background_color,label_color,dir_path, \
data_file_path,filename,ellipsoid_prefs=ellipsoid_prefs, \
add_vectors=add_vectors, plot_scaled=plot_scaled, \
plot_unscaled=plot_unscaled)
def get_denoiser_data_dir():
"""Return the directory of the denoiser error profiles.
"""
dir = get_qiime_project_dir() + "/qiime/support_files/denoiser/Data/"
return dir
def main():
print "\nWarning: compare_3d_plots.py is being deprecated in favor of make_emperor.py, and will no longer be available in QIIME 1.8.0-dev.\n"
option_parser, opts, args = parse_command_line_parameters(**script_info)
prefs, data, background_color, label_color, ball_scale, arrow_colors = sample_color_prefs_and_map_data_from_options(
opts
)
if len(opts.coord_fnames) < 2 and opts.edges_file is None:
option_parser.error("Please provide at least two " + "coordinate files or a custom edges file")
# Open and get coord data (for multiple coords files)
coord_files = opts.coord_fnames
coord_files_valid = validate_coord_files(coord_files)
if not coord_files_valid:
option_parser.error("Every line of every coord file must " + "have the same number of columns.")
num_coord_files = len(coord_files)
data["edges"], data["coord"] = get_multiple_coords(coord_files, opts.edges_file, opts.serial)
# if the edges file wasn't supplied, we appended _i to each file's samples
# therefore we now add duplicated samples with _0, _1,... to mapping file
if opts.edges_file is None:
newmap = [data["map"][0]]
for i in xrange(len(coord_files)):
for sample in data["map"][1:]:
newsample = ["%s_%d" % (sample[0], i)]
newsample.extend(sample[1:])
newmap.append(newsample)
data["map"] = newmap
# remove any samples not present in mapping file
remove_unmapped_samples(data["map"], data["coord"], data["edges"])
if len(data["coord"][1]) == 0:
raise ValueError, "\n\nError: None of the sample IDs in the coordinates files were present in the mapping file.\n"
# process custom axes, if present.
custom_axes = None
if opts.custom_axes:
custom_axes = process_custom_axes(opts.custom_axes)
get_custom_coords(custom_axes, data["map"], data["coord"])
remove_nans(data["coord"])
scale_custom_coords(custom_axes, data["coord"])
# Generate random output file name and create directories
if opts.output_dir:
create_dir(opts.output_dir)
dir_path = opts.output_dir
else:
dir_path = "./"
qiime_dir = get_qiime_project_dir()
jar_path = os.path.join(qiime_dir, "qiime/support_files/jar/")
data_dir_path = get_random_directory_name(output_dir=dir_path, return_absolute_path=False)
try:
os.mkdir(data_dir_path)
except OSError:
pass
jar_dir_path = os.path.join(dir_path, "jar")
try:
os.mkdir(jar_dir_path)
except OSError:
pass
shutil.copyfile(os.path.join(jar_path, "king.jar"), os.path.join(jar_dir_path, "king.jar"))
filepath = coord_files[0]
filename = filepath.strip().split("/")[-1]
try:
action = generate_3d_plots
except NameError:
action = None
# Place this outside try/except so we don't mask NameError in action
if action:
generate_3d_plots(
prefs,
data,
custom_axes,
background_color,
label_color,
dir_path,
data_dir_path,
filename,
ball_scale=ball_scale,
arrow_colors=arrow_colors,
user_supplied_edges=not (opts.edges_file is None),
)
def setUp(self):
""" """
self.qiime_config = load_qiime_config()
self.dirs_to_remove = []
self.files_to_remove = []
# Cannot use get_qiime_project_dir() due to test errors in virtual box
test_dir = os.path.join(get_qiime_project_dir(),'tests')
sff_original_fp = os.path.join(test_dir, 'support_files', \
'Fasting_subset.sff')
# copy sff file to working directory
self.sff_dir = tempfile.mkdtemp()
self.dirs_to_remove.append(self.sff_dir)
self.sff_fp = os.path.join(self.sff_dir, 'Fasting_subset.sff')
copy(sff_original_fp, self.sff_fp)
self.files_to_remove.append(self.sff_fp)
tmp_dir = self.qiime_config['temp_dir'] or '/tmp/'
if not exists(tmp_dir):
makedirs(tmp_dir)
# if test creates the temp dir, also remove it
self.dirs_to_remove.append(tmp_dir)
self.wf_out = get_tmp_filename(tmp_dir=tmp_dir,
prefix='qiime_wf_out',suffix='',result_constructor=str)
self.dirs_to_remove.append(self.wf_out)
self.fasting_mapping_fp = get_tmp_filename(tmp_dir=tmp_dir,
prefix='qiime_wf_mapping',suffix='.txt')
fasting_mapping_f = open(self.fasting_mapping_fp,'w')
fasting_mapping_f.write(fasting_map)
fasting_mapping_f.close()
self.files_to_remove.append(self.fasting_mapping_fp)
'''
self.fasting_seqs_fp = get_tmp_filename(tmp_dir=tmp_dir,
prefix='qiime_wf_seqs',suffix='.fasta')
fasting_seqs_f = open(self.fasting_seqs_fp,'w')
fasting_seqs_f.write(fasting_seqs_subset)
fasting_seqs_f.close()
self.files_to_remove.append(self.fasting_seqs_fp)
self.fasting_seqs_denoiser_fp = get_tmp_filename(tmp_dir=tmp_dir,
prefix='qiime_wf_seqs',suffix='.fasta')
fasting_seqs_f = open(self.fasting_seqs_denoiser_fp,'w')
fasting_seqs_f.write('\n'.join(fasting_seqs_subset.split('\n')[:44]))
fasting_seqs_f.close()
self.files_to_remove.append(self.fasting_seqs_denoiser_fp)
'''
working_dir = self.qiime_config['working_dir'] or './'
jobs_dir = join(working_dir,'jobs')
if not exists(jobs_dir):
# only clean up the jobs dir if it doesn't already exist
self.dirs_to_remove.append(jobs_dir)
self.params = parse_qiime_parameters(qiime_parameters_f)
signal.signal(signal.SIGALRM, timeout)
# set the 'alarm' to go off in allowed_seconds seconds
signal.alarm(allowed_seconds_per_test)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# Some code for error checking of input args:
# Check if distance_matrix_file is valid:
try:
d_header, d_mat = parse_distmat(open(opts.distance_matrix_file, "U"))
except:
option_parser.error(
"This does not look like a valid distance matrix file. Please supply a valid distance matrix file using the -d option."
)
if not is_symmetric_and_hollow(d_mat):
option_parser.error("The distance matrix must be symmetric and " "hollow.")
# Check if map_fname is valid:
try:
mapping, m_header, m_comments = parse_mapping_file(open(opts.map_fname, "U"))
except QiimeParseError:
option_parser.error(
"This does not look like a valid metadata mapping file. Please supply a valid mapping file using the -m option."
)
# make sure background_color is valid
if opts.background_color not in ["black", "white"]:
option_parser.error(
"'%s' is not a valid background color. Please pass in either 'black' or 'white' using the -k option."
% (opts.background_color)
)
# make sure prefs file is valid if it exists
if opts.prefs_path is not None:
try:
prefs_file = open(opts.prefs_path, "U").read()
except IOError:
option_parser.error(
"Provided prefs file, '%s', does not exist. Please pass in a valid prefs file with the -p option."
% (opts.prefs_path)
)
if opts.prefs_path is not None:
prefs = parse_prefs_file(prefs_file)
else:
prefs = None
color_prefs, color_data, background_color, label_color, ball_scale, arrow_colors = sample_color_prefs_and_map_data_from_options(
opts
)
# list of labelname, groups, colors, data_colors, data_color_order
groups_and_colors = list(iter_color_groups(mapping=color_data["map"], prefs=color_prefs))
# dict mapping labelname to list of: [groups, colors, data_colors,
# data_color_order]
field_to_colors = {}
for color_info in groups_and_colors:
field_to_colors[color_info[0]] = color_info[1:]
qiime_dir = get_qiime_project_dir() + "/qiime/support_files/"
fields = opts.fields
if fields is not None:
fields = map(strip, fields.split(","))
fields = [i.strip('"').strip("'") for i in fields]
elif prefs is not None:
fields = prefs.get("FIELDS", None)
else:
fields = get_interesting_mapping_fields(mapping, m_header)
# Check that all provided fields are valid:
if fields is not None:
for f in fields:
if f not in m_header:
option_parser.error(
"The field, %s, is not in the provided mapping file. Please supply correct fields (using the -f option or providing a 'FIELDS' list in the prefs file) corresponding to fields in mapping file."
% (f)
)
within_distances, between_distances, dmat = group_distances(
mapping_file=opts.map_fname,
dmatrix_file=opts.distance_matrix_file,
fields=fields,
dir_prefix=get_random_directory_name(output_dir=opts.dir_path, prefix="distances"),
)
if not opts.suppress_html_output:
# histograms output path
histograms_path = path.join(opts.dir_path, "histograms")
try:
mkdir(histograms_path)
except OSError: # raised if dir exists
pass
# draw all histograms
distances_dict, label_to_histogram_filename = draw_all_histograms(
single_field=within_distances,
paired_field=between_distances,
dmat=dmat,
histogram_dir=histograms_path,
field_to_color_prefs=field_to_colors,
background_color=background_color,
)
# Get relative path to histogram files.
label_to_histogram_filename_relative = _make_relative_paths(label_to_histogram_filename, opts.dir_path)
dm_fname = path.split(opts.distance_matrix_file)[-1]
basename = path.splitext(dm_fname)[0]
outfile_name = basename + "_distance_histograms.html"
make_main_html(
distances_dict=distances_dict,
label_to_histogram_filename=label_to_histogram_filename_relative,
root_outdir=opts.dir_path,
outfile_name=outfile_name,
title="Distance Histograms",
)
# Handle saving web resources locally.
# javascript file
javascript_path = path.join(opts.dir_path, "js")
try:
mkdir(javascript_path)
except OSError: # raised if dir exists
pass
js_out = open(javascript_path + "/histograms.js", "w")
js_out.write(open(qiime_dir + "js/histograms.js").read())
js_out.close()
monte_carlo_iters = opts.monte_carlo_iters
if monte_carlo_iters > 0:
# Do Monte Carlo for all fields
monte_carlo_group_distances(
mapping_file=opts.map_fname,
dmatrix_file=opts.distance_matrix_file,
prefs=prefs,
dir_prefix=opts.dir_path,
fields=fields,
default_iters=monte_carlo_iters,
)
# Do Monte Carlo for within and between fields
monte_carlo_group_distances_within_between(
single_field=within_distances,
paired_field=between_distances,
dmat=dmat,
dir_prefix=opts.dir_path,
num_iters=monte_carlo_iters,
)
def check_mapping_file(mapping_fp,
output_dir=".",
has_barcodes=True,
char_replace="_",
verbose=True,
variable_len_barcodes=False,
disable_primer_check=False,
added_demultiplex_field=None,
suppress_html=False):
""" Main program function for checking mapping file
Checks mapping file for errors, warnings, writes log file, html file,
and corrected mapping file.
mapping_fp: path to metadata mapping file
output_dir: output directory for log, html, corrected mapping file.
has_barcodes: If True, will test for perform barcodes test (presence,
uniqueness, valid IUPAC DNA chars).
char_replace: Character used to replace invalid characters in data
fields. SampleIDs always use periods to be MIENS compliant.
verbose: If True, a message about warnings and/or errors will be printed
to stdout.
variable_len_barcodes: If True, suppresses warnings about barcodes of
varying length.
disable_primer_check: If True, disables tests for valid primer sequences.
added_demultiplex_field: If specified, references a field in the mapping
file to use for demultiplexing. These are to be read from fasta labels
during the actual demultiplexing step. All combinations of barcodes,
primers, and the added_demultiplex_field must be unique."""
header, mapping_data, run_description, errors, warnings =\
process_id_map(open(mapping_fp, 'U'), disable_primer_check,
has_barcodes, char_replace, variable_len_barcodes,
added_demultiplex_field, strip_quotes=False, suppress_stripping=True)
if not suppress_html:
formatted_html = format_mapping_html_data(header, mapping_data,
errors, warnings)
output_html = join(output_dir +
basename(mapping_fp).replace('.txt', '') + ".html")
html_f = open(output_html, "w")
html_f.write(formatted_html)
# get QIIME directory
qiime_dir = get_qiime_project_dir()
# Write javascript file necessary for mouseover tooltips.
# move javascript file to javascript output directory
copyfile(join(qiime_dir, 'qiime', 'support_files',
'js/overlib.js'), join(output_dir, 'overlib.js'))
corrected_mapping_data = correct_mapping_data(mapping_data,
header, char_replace)
output_corrected_fp = join(output_dir +
basename(mapping_fp).replace('.txt', '') + "_corrected.txt")
write_corrected_mapping(output_corrected_fp, header, run_description,
corrected_mapping_data)
output_log_fp = join(output_dir +
basename(mapping_fp).replace('.txt', '') + ".log")
write_log_file(output_log_fp, errors, warnings)
if verbose:
if errors or warnings:
print "Errors and/or warnings detected in mapping file. Please " +\
"check the log and html file for details."
else:
print "No errors or warnings were found in mapping file."
def check_mapping_file(mapping_fp,
output_dir=".",
has_barcodes=True,
char_replace="_",
verbose=True,
variable_len_barcodes=False,
disable_primer_check=False,
added_demultiplex_field=None):
""" Main program function for checking mapping file
Checks mapping file for errors, warnings, writes log file, html file,
and corrected mapping file.
mapping_fp: path to metadata mapping file
output_dir: output directory for log, html, corrected mapping file.
has_barcodes: If True, will test for perform barcodes test (presence,
uniqueness, valid IUPAC DNA chars).
char_replace: Character used to replace invalid characters in data
fields. SampleIDs always use periods to be MIENS compliant.
verbose: If True, a message about warnings and/or errors will be printed
to stdout.
variable_len_barcodes: If True, suppresses warnings about barcodes of
varying length.
disable_primer_check: If True, disables tests for valid primer sequences.
added_demultiplex_field: If specified, references a field in the mapping
file to use for demultiplexing. These are to be read from fasta labels
during the actual demultiplexing step. All combinations of barcodes,
primers, and the added_demultiplex_field must be unique."""
header, mapping_data, run_description, errors, warnings =\
process_id_map(open(mapping_fp, 'U'), disable_primer_check,
has_barcodes, char_replace, variable_len_barcodes,
added_demultiplex_field)
formatted_html = format_mapping_html_data(header, mapping_data,
errors, warnings)
output_html = join(output_dir +\
basename(mapping_fp).replace('.txt', '') + ".html")
html_f = open(output_html, "w")
html_f.write(formatted_html)
#get QIIME directory
qiime_dir=get_qiime_project_dir()
# Write javascript file necessary for mouseover tooltips.
# move javascript file to javascript output directory
copyfile(join(qiime_dir,'qiime','support_files',\
'js/overlib.js'), join(output_dir,'overlib.js'))
corrected_mapping_data = correct_mapping_data(mapping_data,
header, char_replace)
output_corrected_fp = join(output_dir +\
basename(mapping_fp).replace('.txt', '') + "_corrected.txt")
write_corrected_mapping(output_corrected_fp, header, run_description,
corrected_mapping_data)
output_log_fp = join(output_dir +\
basename(mapping_fp).replace('.txt', '') + ".log")
write_log_file(output_log_fp, errors, warnings)
if verbose:
if errors or warnings:
print "Errors and/or warnings detected in mapping file. Please "+\
"check the log and html file for details."
else:
print "No errors or warnings were found in mapping file."
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
#Some code for error checking of input args:
#Check if distance_matrix_file is valid:
try:
d_header, d_mat = parse_distmat(open(opts.distance_matrix_file, 'U'))
except:
option_parser.error(
"This does not look like a valid distance matrix file. Please supply a valid distance matrix file using the -d option."
)
if not is_symmetric_and_hollow(d_mat):
option_parser.error("The distance matrix must be symmetric and "
"hollow.")
#Check if map_fname is valid:
try:
mapping, m_header, m_comments = \
parse_mapping_file(open(opts.map_fname,'U'))
except QiimeParseError:
option_parser.error(
"This does not look like a valid metadata mapping file. Please supply a valid mapping file using the -m option."
)
#make sure background_color is valid
if opts.background_color not in ['black', 'white']:
option_parser.error(
"'%s' is not a valid background color. Please pass in either 'black' or 'white' using the -k option."
% (opts.background_color))
#make sure prefs file is valid if it exists
if opts.prefs_path is not None:
try:
prefs_file = open(opts.prefs_path, 'U').read()
except IOError:
option_parser.error(
"Provided prefs file, '%s', does not exist. Please pass in a valid prefs file with the -p option."
% (opts.prefs_path))
if opts.prefs_path is not None:
prefs = parse_prefs_file(prefs_file)
else:
prefs = None
color_prefs, color_data, background_color, label_color, ball_scale,\
arrow_colors=sample_color_prefs_and_map_data_from_options(opts)
#list of labelname, groups, colors, data_colors, data_color_order
groups_and_colors=list(iter_color_groups(mapping=color_data['map'],\
prefs=color_prefs))
#dict mapping labelname to list of: [groups, colors, data_colors,
# data_color_order]
field_to_colors = {}
for color_info in groups_and_colors:
field_to_colors[color_info[0]] = color_info[1:]
qiime_dir = get_qiime_project_dir() + '/qiime/support_files/'
fields = opts.fields
if fields is not None:
fields = map(strip, fields.split(','))
fields = [i.strip('"').strip("'") for i in fields]
elif prefs is not None:
fields = prefs.get('FIELDS', None)
else:
fields = get_interesting_mapping_fields(mapping, m_header)
#Check that all provided fields are valid:
if fields is not None:
for f in fields:
if f not in m_header:
option_parser.error(
"The field, %s, is not in the provided mapping file. Please supply correct fields (using the -f option or providing a 'FIELDS' list in the prefs file) corresponding to fields in mapping file."
% (f))
within_distances, between_distances, dmat = \
group_distances(mapping_file=opts.map_fname,\
dmatrix_file=opts.distance_matrix_file,\
fields=fields,\
dir_prefix=get_random_directory_name(output_dir=opts.dir_path,\
prefix='distances'))
if not opts.suppress_html_output:
#histograms output path
histograms_path = path.join(opts.dir_path, 'histograms')
try:
mkdir(histograms_path)
except OSError: #raised if dir exists
pass
#draw all histograms
distances_dict, label_to_histogram_filename = \
draw_all_histograms(single_field=within_distances, \
paired_field=between_distances, \
dmat=dmat,\
histogram_dir=histograms_path,\
field_to_color_prefs=field_to_colors,\
background_color=background_color)
#Get relative path to histogram files.
label_to_histogram_filename_relative = \
_make_relative_paths(label_to_histogram_filename, opts.dir_path)
dm_fname = path.split(opts.distance_matrix_file)[-1]
basename = path.splitext(dm_fname)[0]
outfile_name = basename + '_distance_histograms.html'
make_main_html(distances_dict=distances_dict,\
label_to_histogram_filename=label_to_histogram_filename_relative,\
root_outdir=opts.dir_path, \
outfile_name = outfile_name, \
title='Distance Histograms')
#Handle saving web resources locally.
#javascript file
javascript_path = path.join(opts.dir_path, 'js')
try:
mkdir(javascript_path)
except OSError: #raised if dir exists
pass
js_out = open(javascript_path + '/histograms.js', 'w')
js_out.write(open(qiime_dir + 'js/histograms.js').read())
js_out.close()
monte_carlo_iters = opts.monte_carlo_iters
if monte_carlo_iters > 0:
#Do Monte Carlo for all fields
monte_carlo_group_distances(mapping_file=opts.map_fname,\
dmatrix_file=opts.distance_matrix_file,\
prefs=prefs, \
dir_prefix = opts.dir_path,\
fields=fields,\
default_iters=monte_carlo_iters)
#Do Monte Carlo for within and between fields
monte_carlo_group_distances_within_between(\
single_field=within_distances,\
paired_field=between_distances, dmat=dmat, \
dir_prefix = opts.dir_path,\
num_iters=monte_carlo_iters)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
data = {}
# Open and get coord 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:
otu_table = get_log_transform(otu_table)
num_otu_hits = 0
fractional_values = False
max_val = -1
for val in otu_table.iter_data(axis='observation'):
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 opts.tree is not 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 opts.sample_tree is not 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 opts.map_fname is not None:
lines = open(opts.map_fname, 'U').readlines()
map = parse_mapping_file(lines)[0]
ordered_sample_names = [row[0] for row in map]
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)
if (opts.suppress_unit_tests and opts.suppress_script_usage_tests):
option_parser.error(
"You're suppressing both test types. Nothing to run.")
test_dir = abspath(dirname(__file__))
unittest_good_pattern = re.compile('OK\s*$')
application_not_found_pattern = re.compile('ApplicationNotFoundError')
python_name = 'python'
bad_tests = []
missing_application_tests = []
# Run through all of QIIME's unit tests, and keep track of any files which
# fail unit tests.
if not opts.suppress_unit_tests:
unittest_names = []
if not opts.unittest_glob:
for root, dirs, files in walk(test_dir):
for name in files:
if name.startswith('test_') and name.endswith('.py'):
unittest_names.append(join(root, name))
else:
for fp in glob(opts.unittest_glob):
fn = split(fp)[1]
if fn.startswith('test_') and fn.endswith('.py'):
unittest_names.append(abspath(fp))
unittest_names.sort()
for unittest_name in unittest_names:
print "Testing %s:\n" % unittest_name
command = '%s %s -v' % (python_name, unittest_name)
stdout, stderr, return_value = qiime_system_call(command)
print stderr
if not unittest_good_pattern.search(stderr):
if application_not_found_pattern.search(stderr):
missing_application_tests.append(unittest_name)
else:
bad_tests.append(unittest_name)
qiime_test_data_dir = join(get_qiime_project_dir(), 'qiime_test_data')
qiime_test_data_dir_exists = exists(qiime_test_data_dir)
if not opts.suppress_script_usage_tests and qiime_test_data_dir_exists:
if opts.script_usage_tests is not None:
script_usage_tests = opts.script_usage_tests.split(',')
else:
script_usage_tests = None
# Run the script usage testing functionality
script_usage_result_summary, has_script_usage_example_failures = \
run_script_usage_tests(
test_data_dir=qiime_test_data_dir,
scripts_dir=get_qiime_scripts_dir(),
working_dir=qiime_config['temp_dir'],
verbose=True,
tests=script_usage_tests,
force_overwrite=True,
timeout=240)
print "==============\nResult summary\n=============="
if not opts.suppress_unit_tests:
print "\nUnit test result summary\n------------------------\n"
if bad_tests:
print "\nFailed the following unit tests.\n%s" % '\n'.join(bad_tests)
if missing_application_tests:
print "\nFailed the following unit tests, in part or whole due " +\
"to missing external applications.\nDepending on the QIIME features " +\
"you plan to use, this may not be critical.\n%s"\
% '\n'.join(missing_application_tests)
if not (missing_application_tests or bad_tests):
print "\nAll unit tests passed.\n\n"
if not opts.suppress_script_usage_tests:
if qiime_test_data_dir_exists:
print "\nScript usage test result summary\n--------------------------------\n"
print script_usage_result_summary
else:
print "\nCould not run script usage tests because the directory %s does not exist." % qiime_test_data_dir
print ""
# If script usage tests weren't suppressed, the qiime_test_data dir must
# exist and we can't have any failures.
script_usage_tests_success = (opts.suppress_script_usage_tests or
(qiime_test_data_dir_exists and
not has_script_usage_example_failures))
# If any of the unit tests or script usage tests fail, or if we have any
# missing application errors, use return code 1 (as python's unittest
# module does to indicate one or more failures).
return_code = 1
if (len(bad_tests) == 0 and len(missing_application_tests) == 0 and
script_usage_tests_success):
return_code = 0
return return_code
def get_flowgram_ali_exe():
"""Return the path to the flowgram alignment prog
"""
fp = get_qiime_project_dir() +\
"/qiime/support_files/denoiser/bin/FlowgramAli_4frame"
return fp
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
#Check the version of Matplotlib
matplotlib_version = re.split("[^\d]", matplotlib.__version__)
matplotlib_version_info = tuple([int(i) for i in matplotlib_version if \
i.isdigit()])
if matplotlib_version_info != (1,1,0):
print "This code was only tested with Matplotlib-1.1.0"
#get QIIME directory
qiime_dir=get_qiime_project_dir()
if not opts.counts_fname:
option_parser.error("A list of input files must be specified")
#get color preferences
color_prefs, color_data, background_color, label_color= \
taxonomy_color_prefs_and_map_data_from_options(opts)
colorby = opts.colorby
if colorby==None:
colorby=[]
for c in color_data['counts'].values():
colorby.extend(c[0])
else:
colorby=colorby.strip().strip("'").split(',')
counts_fname = opts.counts_fname
#Define labels to use
labels = opts.labels
if not opts.labels:
new_labels=[]
#create an empty list since the user didn't specify labels
for i in counts_fname:
new_labels.append("")
labels=','.join(new_labels)
data = [(label,f.strip()) \
for f,label in zip(counts_fname,labels.split(","))]
filepath=data[0][1]
filename=filepath.strip().rpartition('/')[0]
num_categories = int(opts.num_categories)
if num_categories<=0:
raise ValueError, 'The number of categories has to be greater than 0!'
#create directory path
dir_path = os.getcwd()
if opts.dir_path:
dir_path = opts.dir_path
try:
create_dir(opts.dir_path)
except OSError:
pass
#make javascript output directory
javascript_path = os.path.join(dir_path,'js')
try:
create_dir(javascript_path)
except OSError: #raised if dir exists
pass
#make raw_data output directory
raw_data_path = os.path.join(dir_path,'raw_data')
try:
create_dir(raw_data_path)
except OSError: #raised if dir exists
pass
# move javascript file to javascript output directory
shutil.copyfile(os.path.join(qiime_dir,'qiime','support_files',\
'js/overlib.js'),\
os.path.join(javascript_path,'overlib.js'))
#make css output directory
css_path = os.path.join(dir_path,'css')
try:
create_dir(css_path)
except OSError: #raised if dir exists
pass
# move css file to css output directory
shutil.copyfile(os.path.join(qiime_dir,'qiime','support_files',\
'css/qiime_style.css'),\
os.path.join(css_path,'qiime_style.css'))
# verify all parameters are valid
plot_width=float(opts.x_width)
if plot_width<=0:
raise ValueError, 'The width of the plot has to be greater than 0!'
plot_height=float(opts.y_height)
if plot_height<=0:
raise ValueError, 'The height of the plot has to be greater than 0!'
bar_width=float(opts.bar_width)
if bar_width<=0 or bar_width>1:
raise ValueError, 'The bar width of the plot has to be between 0 and 1!'
dpi=float(opts.dpi)
if dpi<=0:
raise ValueError, 'The dpi of the plot has to be greater than 0!'
resize_nth_label=int(opts.resize_nth_label)
if resize_nth_label<0:
raise ValueError, 'The resize_nth_label of the plot has to be greater than 0!'
generate_image_type=opts.type_of_file
label_type=opts.label_type
include_html_legend=opts.include_html_legend
include_html_counts=opts.include_html_counts
plots_to_make=opts.chart_type.split(',')
chart_types=['area','pie','bar']
for i in plots_to_make:
chart_type=i.lower().strip()
if chart_type not in chart_types:
raise ValueError, 'Please type in one of the appropriate chart types (i.e. %s)!' % ','.join(chart_types)
#make pie chart output path
charts_path = os.path.join(dir_path,'charts')
try:
create_dir(charts_path)
except OSError: #raised if dir exists
pass
make_all_charts(data,dir_path,filename,num_categories, \
colorby,args,color_data, color_prefs,background_color,label_color,\
chart_type,generate_image_type,plot_width,plot_height,bar_width,dpi,\
resize_nth_label,label_type,include_html_legend,include_html_counts)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
data = {}
prefs,data,background_color,label_color,ball_scale, arrow_colors= \
sample_color_prefs_and_map_data_from_options(opts)
data['ellipsoid_method'] = opts.ellipsoid_method
if 0.00 <= opts.ellipsoid_opacity <= 1.00:
data['alpha'] = opts.ellipsoid_opacity
else:
raise ValueError, 'The opacity must be a value between 0 and 1!'
#Open and get coord data
if os.path.isdir(opts.coord_fname) and opts.master_pcoa:
data['coord'], data['support_pcoas'] = load_pcoa_files(
opts.coord_fname)
data['coord'] = get_coord(opts.master_pcoa)
elif os.path.isdir(opts.coord_fname):
data['coord'], data['support_pcoas'] = load_pcoa_files(
opts.coord_fname)
else:
data['coord'] = get_coord(opts.coord_fname)
filepath = opts.coord_fname
basename, extension = os.path.splitext(filepath)
filename = '%s_2D_PCoA_plots' % (basename)
qiime_dir = get_qiime_project_dir()
js_path = os.path.join(qiime_dir, 'qiime', 'support_files', 'js')
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 = './'
html_dir_path = dir_path
data_dir_path = get_random_directory_name(output_dir=dir_path)
try:
os.mkdir(data_dir_path)
except OSError:
pass
js_dir_path = os.path.join(html_dir_path, 'js')
try:
os.mkdir(js_dir_path)
except OSError:
pass
shutil.copyfile(os.path.join(js_path,'overlib.js'), \
os.path.join(js_dir_path,'overlib.js'))
try:
action = generate_2d_plots
except NameError:
action = None
#Place this outside try/except so we don't mask NameError in action
if action:
action(prefs, data, html_dir_path, data_dir_path, filename,
background_color, label_color, opts.scree)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
data = {}
prefs, data, background_color, label_color, ball_scale, arrow_colors = sample_color_prefs_and_map_data_from_options(
opts
)
data["ellipsoid_method"] = opts.ellipsoid_method
if 0.00 <= opts.ellipsoid_opacity <= 1.00:
data["alpha"] = opts.ellipsoid_opacity
else:
raise ValueError("The opacity must be a value between 0 and 1!")
# Open and get coord data
if os.path.isdir(opts.coord_fname) and opts.master_pcoa:
data["coord"], data["support_pcoas"] = load_pcoa_files(opts.coord_fname)
data["coord"] = get_coord(opts.master_pcoa)
elif os.path.isdir(opts.coord_fname):
data["coord"], data["support_pcoas"] = load_pcoa_files(opts.coord_fname)
else:
data["coord"] = get_coord(opts.coord_fname)
filepath = opts.coord_fname
basename, extension = os.path.splitext(filepath)
filename = "%s_2D_PCoA_plots" % (basename)
# obtaining where the files live so they can be copied
qiime_dir = get_qiime_project_dir()
js_path = os.path.join(qiime_dir, "qiime", "support_files", "js")
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 = "./"
html_dir_path = dir_path
data_dir_path = mkdtemp(dir=dir_path)
try:
os.mkdir(data_dir_path)
except OSError:
pass
js_dir_path = os.path.join(html_dir_path, "js")
try:
os.mkdir(js_dir_path)
except OSError:
pass
shutil.copyfile(os.path.join(js_path, "overlib.js"), os.path.join(js_dir_path, "overlib.js"))
try:
action = generate_2d_plots
except NameError:
action = None
# Place this outside try/except so we don't mask NameError in action
if action:
action(
prefs,
data,
html_dir_path,
data_dir_path,
filename,
background_color,
label_color,
opts.scree,
opts.pct_variation_below_one,
)
def _get_R_script_dir(self):
"""Returns the path to the qiime R source directory
"""
qiime_dir = get_qiime_project_dir()
script_dir = join(qiime_dir,'qiime','support_files','R')
return script_dir
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)
def _get_R_script_dir(self):
"""Returns the path to the qiime R source directory
"""
qiime_dir = get_qiime_project_dir()
script_dir = join(qiime_dir, 'qiime', 'support_files', 'R')
return script_dir
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
prefs, data, background_color, label_color, ball_scale, arrow_colors = sample_color_prefs_and_map_data_from_options(
opts
)
scaling_methods = opts.scaling_method.split(",")
plot_scaled = False
plot_unscaled = False
for i in scaling_methods:
if i.lower() == "scaled":
plot_scaled = True
elif i.lower() == "unscaled":
plot_unscaled = True
if not (plot_scaled or plot_unscaled):
raise ValueError, "You must choose a valid scaling method (scaled or unscaled)"
if opts.output_format == "invue":
# validating the number of points for interpolation
if opts.interpolation_points < 0:
option_parser.error("The --interpolation_points should be " + "greater or equal to 0.")
# make sure that coord file has internally consistent # of columns
coord_files_valid = validate_coord_files(opts.coord_fname)
if not coord_files_valid:
option_parser.error("Every line of every coord file must " + "have the same number of columns.")
# Open and get coord data
data["coord"] = get_coord(opts.coord_fname, opts.ellipsoid_method)
# remove any samples not present in mapping file
remove_unmapped_samples(data["map"], data["coord"])
# if no samples overlapped between mapping file and otu table, exit
if len(data["coord"][0]) == 0:
print "\nError: OTU table and mapping file had no samples in common\n"
exit(1)
if opts.output_dir:
create_dir(opts.output_dir, False)
dir_path = opts.output_dir
else:
dir_path = "./"
filepath = opts.coord_fname
if os.path.isdir(filepath):
coord_files = [fname for fname in os.listdir(filepath) if not fname.startswith(".")]
filename = os.path.split(coord_files[0])[-1]
else:
filename = os.path.split(filepath)[-1]
generate_3d_plots_invue(
prefs, data, dir_path, filename, opts.interpolation_points, opts.polyhedron_points, opts.polyhedron_offset
)
# finish script
return
# Potential conflicts
if not opts.custom_axes is None and os.path.isdir(opts.coord_fname):
# can't do averaged pcoa plots _and_ custom axes in the same plot
option_parser.error(
"Please supply either custom axes or multiple coordinate \
files, but not both."
)
# check that smoothness is an integer between 0 and 3
try:
ellipsoid_smoothness = int(opts.ellipsoid_smoothness)
except:
option_parser.error(
"Please supply an integer ellipsoid smoothness \
value."
)
if ellipsoid_smoothness < 0 or ellipsoid_smoothness > 3:
option_parser.error(
"Please supply an ellipsoid smoothness value \
between 0 and 3."
)
# check that opacity is a float between 0 and 1
try:
ellipsoid_alpha = float(opts.ellipsoid_opacity)
except:
option_parser.error("Please supply a number for ellipsoid opacity.")
if ellipsoid_alpha < 0 or ellipsoid_alpha > 1:
option_parser.error(
"Please supply an ellipsoid opacity value \
between 0 and 1."
)
# check that ellipsoid method is valid
ellipsoid_methods = ["IQR", "sdev"]
if not opts.ellipsoid_method in ellipsoid_methods:
option_parser.error(
"Please supply a valid ellipsoid method. \
Valid methods are: "
+ ", ".join(ellipsoid_methods)
+ "."
)
# gather ellipsoid drawing preferences
ellipsoid_prefs = {}
ellipsoid_prefs["smoothness"] = ellipsoid_smoothness
ellipsoid_prefs["alpha"] = ellipsoid_alpha
# make sure that coord file has internally consistent # of columns
coord_files_valid = validate_coord_files(opts.coord_fname)
if not coord_files_valid:
option_parser.error("Every line of every coord file must " + "have the same number of columns.")
# Open and get coord data
data["coord"] = get_coord(opts.coord_fname, opts.ellipsoid_method)
# remove any samples not present in mapping file
remove_unmapped_samples(data["map"], data["coord"])
# if no samples overlapped between mapping file and otu table, exit
if len(data["coord"][0]) == 0:
print "\nError: OTU table and mapping file had no samples in common\n"
exit(1)
# process custom axes, if present.
custom_axes = None
if opts.custom_axes:
custom_axes = process_custom_axes(opts.custom_axes)
get_custom_coords(custom_axes, data["map"], data["coord"])
remove_nans(data["coord"])
scale_custom_coords(custom_axes, data["coord"])
# process vectors if requested
if opts.add_vectors:
add_vectors = {}
add_vectors["vectors"] = opts.add_vectors.split(",")
add_vectors["weight_by_vector"] = opts.weight_by_vector
if len(add_vectors) > 3:
raise ValueError, "You must add maximum 3 columns but %s" % opts.add_vectors
# Validating Vectors values
if opts.vectors_algorithm:
axes_number = len(data["coord"][1][1])
if opts.vectors_axes < 0 or opts.vectors_axes > axes_number:
raise ValueError, "vectors_algorithm should be between 0 and the max number" + "of samples/pcoa-axes: %d" % len(
data["coord"][1][1]
)
if opts.vectors_axes == 0:
opts.vectors_axes = axes_number
add_vectors["vectors_axes"] = opts.vectors_axes
valid_chars = "_.abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789"
for c in opts.vectors_path:
if c not in valid_chars:
raise ValueError, "vectors_path (%s) has invalid chars" % opts.vectors_path
add_vectors["vectors_output"] = {}
add_vectors["vectors_algorithm"] = opts.vectors_algorithm
add_vectors["eigvals"] = data["coord"][3]
add_vectors["window_size"] = None
# checks specific for the modified first difference algorithm
if add_vectors["vectors_algorithm"] == "wdiff":
try:
add_vectors["window_size"] = int(opts.window_size)
except TypeError:
raise TypeError, "Specify --window_size as an integer"
# sanity check as the value can only be greater or equal to one
if add_vectors["window_size"] < 1:
raise ValueError, "The value of window_size is invalid, " + "the value must be greater than zero, not %d" % add_vectors[
"window_size"
]
else:
add_vectors["vectors_algorithm"] = None
add_vectors["vectors_path"] = opts.vectors_path
else:
add_vectors = None
if opts.taxa_fname != None:
# get taxonomy counts
# get list of sample_ids that haven't been removed
sample_ids = data["coord"][0]
# get taxa summaries for all sample_ids
lineages, taxa_counts = get_taxa(opts.taxa_fname, sample_ids)
data["taxa"] = {}
data["taxa"]["lineages"] = lineages
data["taxa"]["counts"] = taxa_counts
# get average relative abundance of taxa
data["taxa"]["prevalence"] = get_taxa_prevalence(data["taxa"]["counts"])
remove_rare_taxa(data["taxa"], nkeep=opts.n_taxa_keep)
# get coordinates of taxa (weighted mean of sample scores)
data["taxa"]["coord"] = get_taxa_coords(data["taxa"]["counts"], data["coord"][1])
data["taxa"]["coord"]
# write taxa coords if requested
if not opts.biplot_output_file is None:
output = make_biplot_scores_output(data["taxa"])
fout = open(opts.biplot_output_file, "w")
fout.write("\n".join(output))
fout.close()
if opts.output_dir:
create_dir(opts.output_dir, False)
dir_path = opts.output_dir
else:
dir_path = "./"
qiime_dir = get_qiime_project_dir()
jar_path = os.path.join(qiime_dir, "qiime/support_files/jar/")
data_dir_path = get_random_directory_name(output_dir=dir_path, return_absolute_path=False)
try:
os.mkdir(data_dir_path)
except OSError:
pass
data_file_path = data_dir_path
jar_dir_path = os.path.join(dir_path, "jar")
try:
os.mkdir(jar_dir_path)
except OSError:
pass
shutil.copyfile(os.path.join(jar_path, "king.jar"), os.path.join(jar_dir_path, "king.jar"))
filepath = opts.coord_fname
if os.path.isdir(filepath):
coord_files = [fname for fname in os.listdir(filepath) if not fname.startswith(".")]
filename = os.path.split(coord_files[0])[-1]
else:
filename = os.path.split(filepath)[-1]
try:
action = generate_3d_plots
except NameError:
action = None
# Place this outside try/except so we don't mask NameError in action
if action:
action(
prefs,
data,
custom_axes,
background_color,
label_color,
dir_path,
data_file_path,
filename,
ellipsoid_prefs=ellipsoid_prefs,
add_vectors=add_vectors,
plot_scaled=plot_scaled,
plot_unscaled=plot_unscaled,
)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
#get QIIME directory
qiime_dir=get_qiime_project_dir()
if not opts.counts_fname:
option_parser.error("A list of input files must be specified")
#get color preferences
color_prefs, color_data, background_color, label_color= \
taxonomy_color_prefs_and_map_data_from_options(opts)
colorby = opts.colorby
if colorby==None:
colorby=[]
for c in color_data['counts'].values():
colorby.extend(c[0])
else:
colorby=colorby.strip().strip("'").split(',')
counts_fname = opts.counts_fname
#Define labels to use
labels = opts.labels
if not opts.labels:
new_labels=[]
#create an empty list since the user didn't specify labels
for i in counts_fname:
new_labels.append("")
labels=','.join(new_labels)
data = [(label,f.strip()) \
for f,label in zip(counts_fname,labels.split(","))]
filepath=data[0][1]
filename=filepath.strip().rpartition('/')[0]
num_categories = int(opts.num_categories)
if num_categories<=0:
raise ValueError, 'The number of categories has to be greater than 0!'
#create directory path
dir_path = os.getcwd()
if opts.dir_path:
dir_path = opts.dir_path
try:
create_dir(opts.dir_path)
except OSError:
pass
#make javascript output directory
javascript_path = os.path.join(dir_path,'js')
try:
create_dir(javascript_path)
except OSError: #raised if dir exists
pass
#make raw_data output directory
raw_data_path = os.path.join(dir_path,'raw_data')
try:
create_dir(raw_data_path)
except OSError: #raised if dir exists
pass
# move javascript file to javascript output directory
shutil.copyfile(os.path.join(qiime_dir,'qiime','support_files',\
'js/overlib.js'),\
os.path.join(javascript_path,'overlib.js'))
#make css output directory
css_path = os.path.join(dir_path,'css')
try:
create_dir(css_path)
except OSError: #raised if dir exists
pass
# move css file to css output directory
shutil.copyfile(os.path.join(qiime_dir,'qiime','support_files',\
'css/qiime_style.css'),\
os.path.join(css_path,'qiime_style.css'))
# verify all parameters are valid
plot_width=float(opts.x_width)
if plot_width<=0:
raise ValueError, 'The width of the plot has to be greater than 0!'
plot_height=float(opts.y_height)
if plot_height<=0:
raise ValueError, 'The height of the plot has to be greater than 0!'
bar_width=float(opts.bar_width)
if bar_width<=0 or bar_width>1:
raise ValueError, 'The bar width of the plot has to be between 0 and 1!'
dpi=float(opts.dpi)
if dpi<=0:
raise ValueError, 'The dpi of the plot has to be greater than 0!'
resize_nth_label=int(opts.resize_nth_label)
if resize_nth_label<0:
raise ValueError, 'The resize_nth_label of the plot has to be greater\
than 0!'
generate_image_type=opts.type_of_file
label_type=opts.label_type
include_html_legend=opts.include_html_legend
include_html_counts=opts.include_html_counts
plots_to_make=opts.chart_type
for chart_type in plots_to_make:
#make pie chart output path
charts_path = os.path.join(dir_path,'charts')
try:
create_dir(charts_path)
except OSError: #raised if dir exists
pass
make_all_charts(data,dir_path,filename,num_categories, \
colorby,args,color_data, color_prefs,background_color,label_color,\
chart_type,generate_image_type,plot_width,plot_height,bar_width,dpi,\
resize_nth_label,label_type,include_html_legend,include_html_counts)
import signal
import os
from os import remove, rmdir
from shutil import rmtree
from subprocess import Popen, PIPE, STDOUT
from cogent.util.unit_test import TestCase, main
from cogent.parse.fasta import MinimalFastaParser
from qiime.util import get_qiime_project_dir, get_qiime_scripts_dir
from qiime.denoiser.utils import check_flowgram_ali_exe
from qiime.denoiser.preprocess import make_tmp_name
PROJECT_HOME = get_qiime_project_dir()
# timeout handling taken from test_workflow.py
class TimeExceededError(Exception):
pass
allowed_seconds_per_test = 240
def timeout(signum, frame):
raise TimeExceededError, "Test failed to run in allowed time (%d seconds)." % allowed_seconds_per_test
class DenoiserTests(TestCase):
def setUp(self):
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
data = {}
# Open and get coord 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:
otu_table = get_log_transform(otu_table)
num_otu_hits = 0
fractional_values = False
max_val = -1
for val in otu_table.iter_data(axis='observation'):
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 opts.tree is not 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 opts.sample_tree is not 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 opts.map_fname is not None:
lines = open(opts.map_fname, 'U').readlines()
map = parse_mapping_file(lines)[0]
ordered_sample_names = [row[0] for row in map]
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)
import signal
import os
from os import remove, rmdir
from shutil import rmtree
from subprocess import Popen, PIPE, STDOUT
from unittest import TestCase, main
from skbio.parse.sequences import parse_fasta
from qiime.util import get_qiime_project_dir
from qiime.denoiser.utils import check_flowgram_ali_exe
from qiime.denoiser.preprocess import make_tmp_name
PROJECT_HOME = get_qiime_project_dir()
# timeout handling taken from test_workflow.py
class TimeExceededError(Exception):
pass
allowed_seconds_per_test = 240
def timeout(signum, frame):
raise TimeExceededError(
"Test failed to run in allowed time (%d seconds)." %
allowed_seconds_per_test)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
prefs, data, background_color, label_color, ball_scale, arrow_colors = \
sample_color_prefs_and_map_data_from_options(opts)
if len(opts.coord_fnames.split(',')) < 2 and opts.edges_file is None:
option_parser.error('Please provide at least two ' +\
'coordinate files or a custom edges file')
#Open and get coord data (for multiple coords files)
coord_files = process_coord_filenames(opts.coord_fnames)
coord_files_valid = validate_coord_files(coord_files)
if not coord_files_valid:
option_parser.error('Every line of every coord file must ' +\
'have the same number of columns.')
num_coord_files = len(coord_files)
data['edges'], data['coord'] = \
get_multiple_coords(coord_files, opts.edges_file, opts.serial)
# if the edges file wasn't supplied, we appended _i to each file's samples
# therefore we now add duplicated samples with _0, _1,... to mapping file
if opts.edges_file is None:
newmap = [data['map'][0]]
for i in xrange(len(coord_files)):
for sample in data['map'][1:]:
newsample = ['%s_%d' %(sample[0],i)]
newsample.extend(sample[1:])
newmap.append(newsample)
data['map'] = newmap
# remove any samples not present in mapping file
remove_unmapped_samples(data['map'],data['coord'],data['edges'])
if(len(data['coord'][1]) == 0):
raise ValueError, '\n\nError: None of the sample IDs in the coordinates files were present in the mapping file.\n'
# process custom axes, if present.
custom_axes = None
if opts.custom_axes:
custom_axes = process_custom_axes(opts.custom_axes)
get_custom_coords(custom_axes, data['map'], data['coord'])
remove_nans(data['coord'])
scale_custom_coords(custom_axes,data['coord'])
# Generate random output file name and create directories
if opts.output_dir:
create_dir(opts.output_dir)
dir_path = opts.output_dir
else:
dir_path='./'
qiime_dir=get_qiime_project_dir()
jar_path=os.path.join(qiime_dir,'qiime/support_files/jar/')
data_dir_path = get_random_directory_name(output_dir=dir_path,
return_absolute_path=False)
try:
os.mkdir(data_dir_path)
except OSError:
pass
jar_dir_path = os.path.join(dir_path,'jar')
try:
os.mkdir(jar_dir_path)
except OSError:
pass
shutil.copyfile(os.path.join(jar_path,'king.jar'), os.path.join(jar_dir_path,'king.jar'))
filepath=coord_files[0]
filename=filepath.strip().split('/')[-1]
try:
action = generate_3d_plots
except NameError:
action = None
#Place this outside try/except so we don't mask NameError in action
if action:
generate_3d_plots(prefs, data, custom_axes,
background_color, label_color,
dir_path, data_dir_path, filename,
ball_scale=ball_scale, arrow_colors=arrow_colors,
user_supplied_edges=not(opts.edges_file is None))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
prefs, data, background_color, label_color, ball_scale, arrow_colors= \
sample_color_prefs_and_map_data_from_options(opts)
if opts.output_format == 'invue':
# validating the number of points for interpolation
if (opts.interpolation_points<0):
option_parser.error('The --interpolation_points should be ' +\
'greater or equal to 0.')
# make sure that coord file has internally consistent # of columns
coord_files_valid = validate_coord_files(opts.coord_fname)
if not coord_files_valid:
option_parser.error('Every line of every coord file must ' +\
'have the same number of columns.')
coord_files_valid = validate_coord_files(opts.coord_fname)
if not coord_files_valid:
option_parser.error('Every line of every coord file must ' +\
'have the same number of columns.')
#Open and get coord data
data['coord'] = get_coord(opts.coord_fname, opts.ellipsoid_method)
# remove any samples not present in mapping file
remove_unmapped_samples(data['map'],data['coord'])
# if no samples overlapped between mapping file and otu table, exit
if len(data['coord'][0]) == 0:
print "\nError: OTU table and mapping file had no samples in common\n"
exit(1)
if opts.output_dir:
create_dir(opts.output_dir,False)
dir_path=opts.output_dir
else:
dir_path='./'
filepath=opts.coord_fname
if os.path.isdir(filepath):
coord_files = [fname for fname in os.listdir(filepath) if not \
fname.startswith('.')]
filename = os.path.split(coord_files[0])[-1]
else:
filename = os.path.split(filepath)[-1]
generate_3d_plots_invue(prefs, data, dir_path, filename, \
opts.interpolation_points, opts.polyhedron_points, \
opts.polyhedron_offset)
#finish script
return
# Potential conflicts
if not opts.custom_axes is None and os.path.isdir(opts.coord_fname):
# can't do averaged pcoa plots _and_ custom axes in the same plot
option_parser.error("Please supply either custom axes or multiple coordinate \
files, but not both.")
# check that smoothness is an integer between 0 and 3
try:
ellipsoid_smoothness = int(opts.ellipsoid_smoothness)
except:
option_parser.error("Please supply an integer ellipsoid smoothness \
value.")
if ellipsoid_smoothness < 0 or ellipsoid_smoothness > 3:
option_parser.error("Please supply an ellipsoid smoothness value \
between 0 and 3.")
# check that opacity is a float between 0 and 1
try:
ellipsoid_alpha = float(opts.ellipsoid_opacity)
except:
option_parser.error("Please supply a number for ellipsoid opacity.")
if ellipsoid_alpha < 0 or ellipsoid_alpha > 1:
option_parser.error("Please supply an ellipsoid opacity value \
between 0 and 1.")
# check that ellipsoid method is valid
ellipsoid_methods = ['IQR','sdev']
if not opts.ellipsoid_method in ellipsoid_methods:
option_parser.error("Please supply a valid ellipsoid method. \
Valid methods are: " + ', '.join(ellipsoid_methods) + ".")
# gather ellipsoid drawing preferences
ellipsoid_prefs = {}
ellipsoid_prefs["smoothness"] = ellipsoid_smoothness
ellipsoid_prefs["alpha"] = ellipsoid_alpha
# make sure that coord file has internally consistent # of columns
coord_files_valid = validate_coord_files(opts.coord_fname)
if not coord_files_valid:
option_parser.error('Every line of every coord file must ' +\
'have the same number of columns.')
#Open and get coord data
data['coord'] = get_coord(opts.coord_fname, opts.ellipsoid_method)
# remove any samples not present in mapping file
remove_unmapped_samples(data['map'],data['coord'])
# if no samples overlapped between mapping file and otu table, exit
if len(data['coord'][0]) == 0:
print "\nError: OTU table and mapping file had no samples in common\n"
exit(1)
if opts.taxa_fname != None:
# get taxonomy counts
# get list of sample_ids that haven't been removed
sample_ids = data['coord'][0]
# get taxa summaries for all sample_ids
lineages, taxa_counts = get_taxa(opts.taxa_fname, sample_ids)
data['taxa'] = {}
data['taxa']['lineages'] = lineages
data['taxa']['counts'] = taxa_counts
# get average relative abundance of taxa
data['taxa']['prevalence'] = get_taxa_prevalence(data['taxa']['counts'])
remove_rare_taxa(data['taxa'],nkeep=opts.n_taxa_keep)
# get coordinates of taxa (weighted mean of sample scores)
data['taxa']['coord'] = get_taxa_coords(data['taxa']['counts'],
data['coord'][1])
data['taxa']['coord']
# write taxa coords if requested
if not opts.biplot_output_file is None:
output = make_biplot_scores_output(data['taxa'])
fout = open(opts.biplot_output_file,'w')
fout.write('\n'.join(output))
fout.close()
# process custom axes, if present.
custom_axes = None
if opts.custom_axes:
custom_axes = process_custom_axes(opts.custom_axes)
get_custom_coords(custom_axes, data['map'], data['coord'])
remove_nans(data['coord'])
scale_custom_coords(custom_axes,data['coord'])
if opts.output_dir:
create_dir(opts.output_dir,False)
dir_path=opts.output_dir
else:
dir_path='./'
qiime_dir=get_qiime_project_dir()
jar_path=os.path.join(qiime_dir,'qiime/support_files/jar/')
data_dir_path = get_random_directory_name(output_dir=dir_path,
return_absolute_path=False)
try:
os.mkdir(data_dir_path)
except OSError:
pass
data_file_path=data_dir_path
jar_dir_path = os.path.join(dir_path,'jar')
try:
os.mkdir(jar_dir_path)
except OSError:
pass
shutil.copyfile(os.path.join(jar_path,'king.jar'), os.path.join(jar_dir_path,'king.jar'))
filepath=opts.coord_fname
if os.path.isdir(filepath):
coord_files = [fname for fname in os.listdir(filepath) if not \
fname.startswith('.')]
filename = os.path.split(coord_files[0])[-1]
else:
filename = os.path.split(filepath)[-1]
try:
action = generate_3d_plots
except NameError:
action = None
#Place this outside try/except so we don't mask NameError in action
if action:
action(prefs,data,custom_axes,background_color,label_color,dir_path, \
data_file_path,filename,ellipsoid_prefs=ellipsoid_prefs)