invalid literal for float(): 4 # Discard taxa representing nodes in the phylogenetic tree not

[wonitawowowo]

Hellow
I want to try mitre.WIth you example, It runs will,but when I want to try it on my data,some errors rised.
my pplacer version:
pplacer --version
v1.1.alpha19-0-g807f6f
my taxit:
taxit --version
taxit v0.9.0

when I run mitre in taxonomy_source = table it would rise:
Traceback (most recent call last):
File "/home/wkz/anaconda3/envs/python27/bin/mitre", line 11, in
load_entry_point('mitre==1.0b1', 'console_scripts', 'mitre')()
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/mitre/command_line.py", line 42, in run
mitre.main.run_from_config_file(args.config_file)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/mitre/main.py", line 64, in run_from_config_file
current_dataset = preprocess(config)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/mitre/main.py", line 272, in preprocess
data = preprocess_step2(config, data)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/mitre/main.py", line 726, in preprocess_step2
data = temporal_filter_if_needed(config, data)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/mitre/main.py", line 245, in temporal_filter_if_needed
'temporal_abundance_n_subjects')
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/ConfigParser.py", line 362, in getfloat
return self._get(section, float, option)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/ConfigParser.py", line 356, in _get
return conv(self.get(section, option))
ValueError: invalid literal for float(): 4 # Discard taxa representing nodes in the phylogenetic tree not

and in taxonomy_source = pplacer it would rise:
Traceback (most recent call last):
File "/home/wkz/anaconda3/envs/python27/bin/mitre", line 11, in
load_entry_point('mitre==1.0b1', 'console_scripts', 'mitre')()
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/mitre/command_line.py", line 42, in run
mitre.main.run_from_config_file(args.config_file)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/mitre/main.py", line 64, in run_from_config_file
current_dataset = preprocess(config)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/mitre/main.py", line 272, in preprocess
data = preprocess_step2(config, data)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/mitre/main.py", line 698, in preprocess_step2
seq_info_filename
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/mitre/load_data/taxonomy_annotation.py", line 37, in annotate_dataset_pplacer
seq_info_filename
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/mitre/load_data/pplacer.py", line 391, in describe_tree_nodes_with_taxonomy
taxa.append(map(tname,values))
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/mitre/load_data/pplacer.py", line 373, in
tname = lambda j: str(taxa_table.loc[j]['tax_name'])
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/pandas/core/indexing.py", line 1500, in getitem
return self._getitem_axis(maybe_callable, axis=axis)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/pandas/core/indexing.py", line 1912, in _getitem_axis
self._validate_key(key, axis)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/pandas/core/indexing.py", line 1799, in _validate_key
self._convert_scalar_indexer(key, axis)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/pandas/core/indexing.py", line 262, in _convert_scalar_indexer
return ax._convert_scalar_indexer(key, kind=self.name)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/pandas/core/indexes/numeric.py", line 211, in _convert_scalar_indexer
._convert_scalar_indexer(key, kind=kind))
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/pandas/core/indexes/base.py", line 2877, in _convert_scalar_indexer
return self._invalid_indexer('label', key)
File "/home/wkz/anaconda3/envs/python27/lib/python2.7/site-packages/pandas/core/indexes/base.py", line 3067, in _invalid_indexer
kind=type(key)))
TypeError: cannot do label indexing on <class 'pandas.core.indexes.numeric.Int64Index'> with these indexers [nan] of <type 'numpy.float64'>

could you give my some suggestion？Thank a lot.

[wonitawowowo]

emmm,I ignore the words followed by #.I copy the .cfg from the PDF without '\n' there.Which lead to the first error.

I still can not do it with taxonomy_source = pplacer metric.