def setUp(self):
self.qiime_config = load_qiime_config()
self.tmp_dir = self.qiime_config['temp_dir'] or '/tmp/'
self.l19_data = numpy.array([[7, 1, 0, 0, 0, 0, 0, 0, 0],
[4, 2, 0, 0, 0, 1, 0, 0, 0],
[2, 4, 0, 0, 0, 1, 0, 0, 0],
[1, 7, 0, 0, 0, 0, 0, 0, 0],
[0, 8, 0, 0, 0, 0, 0, 0, 0],
[0, 7, 1, 0, 0, 0, 0, 0, 0],
[0, 4, 2, 0, 0, 0, 2, 0, 0],
[0, 2, 4, 0, 0, 0, 1, 0, 0],
[0, 1, 7, 0, 0, 0, 0, 0, 0],
[0, 0, 8, 0, 0, 0, 0, 0, 0],
[0, 0, 7, 1, 0, 0, 0, 0, 0],
[0, 0, 4, 2, 0, 0, 0, 3, 0],
[0, 0, 2, 4, 0, 0, 0, 1, 0],
[0, 0, 1, 7, 0, 0, 0, 0, 0],
[0, 0, 0, 8, 0, 0, 0, 0, 0],
[0, 0, 0, 7, 1, 0, 0, 0, 0],
[0, 0, 0, 4, 2, 0, 0, 0, 4],
[0, 0, 0, 2, 4, 0, 0, 0, 1],
[0, 0, 0, 1, 7, 0, 0, 0, 0]])
self.l19_sample_names = ['sam1', 'sam2', 'sam3', 'sam4', 'sam5','sam6',\
'sam7', 'sam8', 'sam9', 'sam_middle', 'sam11', 'sam12', 'sam13', \
'sam14', 'sam15', 'sam16', 'sam17', 'sam18', 'sam19']
self.l19_taxon_names = ['tax1', 'tax2', 'tax3', 'tax4', 'endbigtaxon',\
'tax6', 'tax7', 'tax8', 'tax9']
self.l19_taxon_names_w_underscore = [
'ta_x1', 'tax2', 'tax3', 'tax4', 'endbigtaxon', 'tax6', 'tax7',
'tax8', 'tax9'
]
l19_str = format_biom_table(
DenseOTUTable(self.l19_data.T, self.l19_sample_names,
self.l19_taxon_names))
self.l19_fp = get_tmp_filename(tmp_dir=self.tmp_dir,
prefix='test_bdiv_otu_table',
suffix='.blom')
open(self.l19_fp, 'w').write(l19_str)
l19_str_w_underscore = format_biom_table(
DenseOTUTable(self.l19_data.T, self.l19_sample_names,
self.l19_taxon_names_w_underscore))
self.l19_str_w_underscore_fp = get_tmp_filename(
tmp_dir=self.tmp_dir, prefix='test_bdiv_otu_table', suffix='.blom')
open(self.l19_str_w_underscore_fp, 'w').write(l19_str_w_underscore)
self.l19_tree_str = '((((tax7:0.1,tax3:0.2):.98,tax8:.3, tax4:.3):.4,\
((tax1:0.3, tax6:.09):0.43,tax2:0.4):0.5):.2, (tax9:0.3, endbigtaxon:.08));'
self.l19_tree = parse_newick(self.l19_tree_str, PhyloNode)
self.files_to_remove = [self.l19_fp, self.l19_str_w_underscore_fp]
self.folders_to_remove = []
def format_otu_table(sample_names, otu_names, data, taxonomy=None,
comment=None, skip_empty=False,legacy=True):
"""Returns string representing OTU table as biom file
"""
print "Deprecation Warning: you should not be using format_otu_table. Instead use qiime.format.format_biom_table"
if taxonomy != None:
def strip_f(s):
return s.strip()
taxonomy = [{'taxonomy':map(strip_f,t.split(';'))} for t in taxonomy]
otu_table = DenseOTUTable(Data=data,
SampleIds=sample_names,
ObservationIds=otu_names,
ObservationMetadata=taxonomy)
return format_biom_table(otu_table)