def test_transfer_observation_metadata_moves_observation_metadata_between_biom_tables(self):
"""transfer_sample_metadata moves sample metadata values between BIOM format tables"""
t1 = self.genome_table1
exp = self.genome_table1_with_metadata
actual = transfer_observation_metadata(self.genome_table1_with_metadata,\
self.genome_table1,"observation",verbose=False)
actual_md = map(dict,sorted([md for md in actual.metadata(axis='observation')]))
exp_md = map(dict,sorted([md for md in exp.metadata(axis='observation')]))
for i,md in enumerate(actual_md):
self.assertEqualItems(md,exp_md[i])
for i,md in enumerate(exp_md):
self.assertEqualItems(md,actual_md[i])
def test_transfer_observation_metadata_moves_observation_metadata_between_biom_tables(self):
"""transfer_sample_metadata moves sample metadata values between BIOM format tables"""
t1 = self.genome_table1
exp = self.genome_table1_with_metadata
actual = transfer_observation_metadata(self.genome_table1_with_metadata,\
self.genome_table1,"observation",verbose=False)
actual_md = map(dict,sorted([md for md in actual.metadata(axis='observation')]))
exp_md = map(dict,sorted([md for md in exp.metadata(axis='observation')]))
for i,md in enumerate(actual_md):
self.assertEqualItems(md,exp_md[i])
for i,md in enumerate(exp_md):
self.assertEqualItems(md,actual_md[i])
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
otu_table = load_table(opts.input_otu_fp)
ids_to_load = otu_table.ids(axis='observation')
if(opts.input_count_fp is None):
#precalc file has specific name (e.g. 16S_13_5_precalculated.tab.gz)
precalc_file_name='_'.join(['16S',opts.gg_version,'precalculated.tab.gz'])
input_count_table=join(get_picrust_project_dir(),'picrust','data',precalc_file_name)
else:
input_count_table=opts.input_count_fp
if opts.verbose:
print "Loading trait table: ", input_count_table
ext=path.splitext(input_count_table)[1]
if (ext == '.gz'):
count_table_fh = gzip.open(input_count_table,'rb')
else:
count_table_fh = open(input_count_table,'U')
if opts.load_precalc_file_in_biom:
count_table = load_table(count_table_fh)
else:
count_table = convert_precalc_to_biom(count_table_fh, ids_to_load)
#Need to only keep data relevant to our otu list
ids=[]
for x in otu_table.iter(axis='observation'):
ids.append(str(x[1]))
ob_id=count_table.ids(axis='observation')[0]
filtered_otus=[]
filtered_values=[]
for x in ids:
if count_table.exists(x, axis='sample'):
filtered_otus.append(x)
filtered_values.append(otu_table.data(x, axis='observation'))
filtered_otu_table = Table(filtered_values, filtered_otus, otu_table.ids())
copy_numbers_filtered={}
for x in filtered_otus:
value = count_table.get_value_by_ids(ob_id,x)
try:
#data can be floats so round them and make them integers
value = int(round(float(value)))
except ValueError:
raise ValueError,\
"Invalid type passed as copy number for OTU ID %s. Must be int-able." % (value)
if value < 1:
raise ValueError, "Copy numbers must be greater than or equal to 1."
copy_numbers_filtered[x]={opts.metadata_identifer:value}
filtered_otu_table.add_metadata(copy_numbers_filtered, axis='observation')
def metadata_norm(v, i, md):
return v / float(md[opts.metadata_identifer])
normalized_table = filtered_otu_table.transform(metadata_norm, axis='observation')
#move Observation Metadata from original to filtered OTU table
normalized_table = transfer_observation_metadata(otu_table, normalized_table, 'observation')
make_output_dir_for_file(opts.output_otu_fp)
write_biom_table(normalized_table, opts.output_otu_fp)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
input_ext = path.splitext(opts.input_otu_fp)[1]
if opts.input_format_classic:
otu_table = parse_classic_table_to_rich_table(
open(opts.input_otu_fp, 'U'), None, None, None, DenseOTUTable)
else:
try:
otu_table = parse_biom_table(open(opts.input_otu_fp, 'U'))
except ValueError:
raise ValueError(
"Error loading OTU table! If not in BIOM format use '-f' option.\n"
)
ids_to_load = otu_table.ObservationIds
if (opts.input_count_fp is None):
#precalc file has specific name (e.g. 16S_13_5_precalculated.tab.gz)
precalc_file_name = '_'.join(
['16S', opts.gg_version, 'precalculated.tab.gz'])
input_count_table = join(get_picrust_project_dir(), 'picrust', 'data',
precalc_file_name)
else:
input_count_table = opts.input_count_fp
if opts.verbose:
print "Loading trait table: ", input_count_table
ext = path.splitext(input_count_table)[1]
if (ext == '.gz'):
count_table_fh = gzip.open(input_count_table, 'rb')
else:
count_table_fh = open(input_count_table, 'U')
if opts.load_precalc_file_in_biom:
count_table = parse_biom_table(count_table_fh.read())
else:
count_table = convert_precalc_to_biom(count_table_fh, ids_to_load)
#Need to only keep data relevant to our otu list
ids = []
for x in otu_table.iterObservations():
ids.append(str(x[1]))
ob_id = count_table.ObservationIds[0]
filtered_otus = []
filtered_values = []
for x in ids:
if count_table.sampleExists(x):
filtered_otus.append(x)
filtered_values.append(otu_table.observationData(x))
#filtered_values = map(list,zip(*filtered_values))
filtered_otu_table = table_factory(filtered_values,
otu_table.SampleIds,
filtered_otus,
constructor=DenseOTUTable)
copy_numbers_filtered = {}
for x in filtered_otus:
value = count_table.getValueByIds(ob_id, x)
try:
#data can be floats so round them and make them integers
value = int(round(float(value)))
except ValueError:
raise ValueError,\
"Invalid type passed as copy number for OTU ID %s. Must be int-able." % (value)
if value < 1:
raise ValueError, "Copy numbers must be greater than or equal to 1."
copy_numbers_filtered[x] = {opts.metadata_identifer: value}
filtered_otu_table.addObservationMetadata(copy_numbers_filtered)
normalized_table = filtered_otu_table.normObservationByMetadata(
opts.metadata_identifer)
#move Observation Metadata from original to filtered OTU table
normalized_table = transfer_observation_metadata(otu_table,
normalized_table,
'ObservationMetadata')
normalized_otu_table = transfer_sample_metadata(otu_table,
normalized_table,
'SampleMetadata')
make_output_dir_for_file(opts.output_otu_fp)
open(opts.output_otu_fp, 'w').write(format_biom_table(normalized_table))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
otu_table = load_table(opts.input_otu_fp)
ids_to_load = otu_table.ids(axis="observation")
if opts.input_count_fp is None:
# precalc file has specific name (e.g. 16S_13_5_precalculated.tab.gz)
precalc_file_name = "_".join(["16S", opts.gg_version, "precalculated.tab.gz"])
input_count_table = join(get_picrust_project_dir(), "picrust", "data", precalc_file_name)
else:
input_count_table = opts.input_count_fp
if opts.verbose:
print "Loading trait table: ", input_count_table
ext = path.splitext(input_count_table)[1]
if ext == ".gz":
count_table_fh = gzip.open(input_count_table, "rb")
else:
count_table_fh = open(input_count_table, "U")
if opts.load_precalc_file_in_biom:
count_table = load_table(count_table_fh)
else:
count_table = convert_precalc_to_biom(count_table_fh, ids_to_load)
# Need to only keep data relevant to our otu list
ids = []
for x in otu_table.iter(axis="observation"):
ids.append(str(x[1]))
ob_id = count_table.ids(axis="observation")[0]
filtered_otus = []
filtered_values = []
for x in ids:
if count_table.exists(x, axis="sample"):
filtered_otus.append(x)
filtered_values.append(otu_table.data(x, axis="observation"))
filtered_otu_table = Table(filtered_values, filtered_otus, otu_table.ids())
copy_numbers_filtered = {}
for x in filtered_otus:
value = count_table.get_value_by_ids(ob_id, x)
try:
# data can be floats so round them and make them integers
value = int(round(float(value)))
except ValueError:
raise ValueError, "Invalid type passed as copy number for OTU ID %s. Must be int-able." % (value)
if value < 1:
raise ValueError, "Copy numbers must be greater than or equal to 1."
copy_numbers_filtered[x] = {opts.metadata_identifer: value}
filtered_otu_table.add_metadata(copy_numbers_filtered, axis="observation")
def metadata_norm(v, i, md):
return v / float(md[opts.metadata_identifer])
normalized_table = filtered_otu_table.transform(metadata_norm, axis="observation")
# move Observation Metadata from original to filtered OTU table
normalized_table = transfer_observation_metadata(otu_table, normalized_table, "observation")
make_output_dir_for_file(opts.output_otu_fp)
write_biom_table(normalized_table, opts.output_otu_fp)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
input_ext=path.splitext(opts.input_otu_fp)[1]
if opts.input_format_classic:
otu_table=parse_classic_table_to_rich_table(open(opts.input_otu_fp,'U'),None,None,None,DenseOTUTable)
else:
try:
otu_table = parse_biom_table(open(opts.input_otu_fp,'U'))
except ValueError:
raise ValueError("Error loading OTU table! If not in BIOM format use '-f' option.\n")
ids_to_load = otu_table.ObservationIds
if(opts.input_count_fp is None):
#precalc file has specific name (e.g. 16S_13_5_precalculated.tab.gz)
precalc_file_name='_'.join(['16S',opts.gg_version,'precalculated.tab.gz'])
input_count_table=join(get_picrust_project_dir(),'picrust','data',precalc_file_name)
else:
input_count_table=opts.input_count_fp
if opts.verbose:
print "Loading trait table: ", input_count_table
ext=path.splitext(input_count_table)[1]
if (ext == '.gz'):
count_table_fh = gzip.open(input_count_table,'rb')
else:
count_table_fh = open(input_count_table,'U')
if opts.load_precalc_file_in_biom:
count_table = parse_biom_table(count_table_fh.read())
else:
count_table = convert_precalc_to_biom(count_table_fh,ids_to_load)
#Need to only keep data relevant to our otu list
ids=[]
for x in otu_table.iterObservations():
ids.append(str(x[1]))
ob_id=count_table.ObservationIds[0]
filtered_otus=[]
filtered_values=[]
for x in ids:
if count_table.sampleExists(x):
filtered_otus.append(x)
filtered_values.append(otu_table.observationData(x))
#filtered_values = map(list,zip(*filtered_values))
filtered_otu_table=table_factory(filtered_values,otu_table.SampleIds,filtered_otus, constructor=DenseOTUTable)
copy_numbers_filtered={}
for x in filtered_otus:
value = count_table.getValueByIds(ob_id,x)
try:
#data can be floats so round them and make them integers
value = int(round(float(value)))
except ValueError:
raise ValueError,\
"Invalid type passed as copy number for OTU ID %s. Must be int-able." % (value)
if value < 1:
raise ValueError, "Copy numbers must be greater than or equal to 1."
copy_numbers_filtered[x]={opts.metadata_identifer:value}
filtered_otu_table.addObservationMetadata(copy_numbers_filtered)
normalized_table = filtered_otu_table.normObservationByMetadata(opts.metadata_identifer)
#move Observation Metadata from original to filtered OTU table
normalized_table = transfer_observation_metadata(otu_table,normalized_table,'ObservationMetadata')
normalized_otu_table = transfer_sample_metadata(otu_table,normalized_table,'SampleMetadata')
make_output_dir_for_file(opts.output_otu_fp)
open(opts.output_otu_fp,'w').write(format_biom_table(normalized_table))
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
input_ext=path.splitext(opts.input_otu_fp)[1]
if opts.input_format_classic:
otu_table=parse_classic_table_to_rich_table(open(opts.input_otu_fp,'U'),None,None,None,DenseOTUTable)
else:
try:
otu_table = parse_biom_table(open(opts.input_otu_fp,'U'))
except ValueError:
raise ValueError("Error loading OTU table! If not in BIOM format use '-f' option.\n")
ext=path.splitext(opts.input_count_fp)[1]
if (ext == '.gz'):
count_table = parse_biom_table(gzip.open(opts.input_count_fp,'rb'))
else:
count_table = parse_biom_table(open(opts.input_count_fp,'U'))
#Need to only keep data relevant to our otu list
ids=[]
for x in otu_table.iterObservations():
ids.append(str(x[1]))
ob_id=count_table.ObservationIds[0]
filtered_otus=[]
filtered_values=[]
for x in ids:
if count_table.sampleExists(x):
filtered_otus.append(x)
filtered_values.append(otu_table.observationData(x))
#filtered_values = map(list,zip(*filtered_values))
filtered_otu_table=table_factory(filtered_values,otu_table.SampleIds,filtered_otus, constructor=DenseOTUTable)
copy_numbers_filtered={}
for x in filtered_otus:
value = count_table.getValueByIds(ob_id,x)
try:
#data can be floats so round them and make them integers
value = int(round(float(value)))
except ValueError:
raise ValueError,\
"Invalid type passed as copy number for OTU ID %s. Must be int-able." % (value)
if value < 1:
raise ValueError, "Copy numbers must be greater than or equal to 1."
copy_numbers_filtered[x]={opts.metadata_identifer:value}
filtered_otu_table.addObservationMetadata(copy_numbers_filtered)
normalized_table = filtered_otu_table.normObservationByMetadata(opts.metadata_identifer)
#move Observation Metadata from original to filtered OTU table
normalized_table = transfer_observation_metadata(otu_table,normalized_table,'ObservationMetadata')
normalized_otu_table = transfer_sample_metadata(otu_table,normalized_table,'SampleMetadata')
make_output_dir_for_file(opts.output_otu_fp)
open(opts.output_otu_fp,'w').write(\
normalized_table.getBiomFormatJsonString('PICRUST'))
