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Keyerror: taxonomy #56
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Hi, Thanks, Sandipan |
Hi Zewei, Thanks and any help will be appreciated. Thanks again. Sandipan |
Hi! I had the same error as @maracashay here. Did anyone find a solution to it? |
Hi everyone,
I am working with an ASV table from dada2 output in R. I did some data wrangling to make a 'taxonomy' column as similar as I could to the example asv table provided. I also changed 'ASV' to 'OTU' in case that was important. The taxonomy column in the ASV table looks like this:
|Vishniacozyma_victoriae|k__Fungi;p__Basidiomycota;c__Tremellomycetes;o__Tremellales;f__Bulleribasidiaceae;g__Vishniacozyma;s__victoriae
Here is the error message: FUNGuild % python FUNGuild.py taxa -otu /Users/maraslaptop/Downloads/Fungal-Steam-ASV-Table.txt -format tsv -column taxonomy -classifier unite
Taxa parser initiated.
Loading OTU table: /Users/maraslaptop/Downloads/Fungal-Steam-ASV-Table.txt
Table format: tsv
Taxonomic column: taxonomy
Taxonomic style: unite
Traceback (most recent call last):
File "/opt/anaconda3/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2897, in get_loc
return self._engine.get_loc(key)
File "pandas/_libs/index.pyx", line 107, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 131, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1607, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1614, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'taxonomy'
I'm attaching a shortened version of my asv file.
Fungal-ASV-Funguild.txt
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