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.