# Open FeatureData in Artifact API **URL:** \ **Category:** User Support\ **Tags:** artifact-api\ **Created:** [July 24, 2018, 2:56am UTC](https://forum.qiime2.org/t/open-featuredata-in-artifact-api/5202 "2018-07-24T02:56:17Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![samuel.drouin](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/s/f17d59/32.png) [@samuel.drouin](https://forum.qiime2.org/u/samuel.drouin)\ **Post date:** [July 24, 2018, 2:56am UTC](https://forum.qiime2.org/t/open-featuredata-in-artifact-api/5202/1 "2018-07-24T02:56:17Z")
Hi, I am trying to write a small python script that process MiSeq samples through Qiime 2 with Artifact API and plugins to generate taxonomy data. The steps are as follow : cutadapt -\> import in Qiime 2 -\> DADA2 -\> classifier (classify\_sklearn) -\> output Question 1 : Is it possible to access the FeatureData[Taxonomy] Artifact data (UUID, taxon and confidence level) at the classification step directly in python ? Something like when we generate the TSV file from the visualization but within the script. Question 2 : I tried to export the taxonomy visualization with the following python code : `metadata.visualizers.tabulate(input=classification).visualization.save(os.path.join(directory['Qiime'] + "/taxonomy.qzv"))` Which I assumed would be the equivalent of : `qiime metadata tabulate --m-input-file taxonomy.qza --o-visualization taxonomy.qzv` However I get the following error : `TypeError: Argument to parameter 'input' is not a subtype of Metadata.` Is there any way to export the taxonomy visualization other than export the artifact and use the above command on subprocess to generate the visualization ? Question 3 : Is there any Artifact/plugins API tutorial in the documentation ? I found a lot of informations about the CLI but not much about the API (other than the dev. docs and the Artifact API docs). Thank you ---
**Author:** ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)\ **Post date:** [July 24, 2018, 12:55pm UTC](https://forum.qiime2.org/t/open-featuredata-in-artifact-api/5202/2 "2018-07-24T12:55:56Z")
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**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [July 24, 2018, 1:52pm UTC](https://forum.qiime2.org/t/open-featuredata-in-artifact-api/5202/3 "2018-07-24T13:52:46Z")
Hello @samuel.drouin! > [@samuel.drouin](#): > > Question 1 : Grabbing the UUID is straightforward (just a prop on the `Artifact`), while getting the other parts are pretty simple, too, but only if you know to use the `view` ~~API~~ method (we are lacking good docs in the dept, sorry!) ```python import qiime2 import pandas as pd # here I am loading, but this could also be results passed # down from a previous step. taxonomy_artifact = qiime2.Artifact.load('taxonomy.qza') # Get the UUID of the Artifact print(taxonomy_artifact.uuid) 7224759e-03bb-4179-a382-485165ca8c86 # `view` as a pd.DataFrame to get the taxon and conf. taxonomy_df = taxonomy_artifact.view(pd.DataFrame) print(taxonomy_df.head()) Taxon \ Feature ID 7fa8f515ee1ac5cb8b529b13e6a89790 k __Bacteria; p__ Proteobacteria; c__Gammaproteo... 40f13b077d41d6837ca6fae65763cf01 k __Bacteria; p__ Actinobacteria; c__Actinobacte... 2e55763e77234a7bfc3a311067a0c7e1 k __Bacteria; p__ Firmicutes; c __Clostridia; o__... d5ef913e6aee3067001dc610ac8af1d1 k __Bacteria; p__ Actinobacteria; c__Actinobacte... bc15061b61cf6b5002c58284591f97d4 k __Bacteria; p__ Firmicutes; c __Clostridia; o__... Confidence Feature ID 7fa8f515ee1ac5cb8b529b13e6a89790 0.9998282422613309 40f13b077d41d6837ca6fae65763cf01 0.9999994725274034 2e55763e77234a7bfc3a311067a0c7e1 0.9177375883240979 d5ef913e6aee3067001dc610ac8af1d1 0.9971204554883859 bc15061b61cf6b5002c58284591f97d4 0.9999262723979453 ``` > [@samuel.drouin](#): > > Question 2 You will need to `view` as `qiime2.Metadata`, first: ```python import qiime2 from qiime2.plugins import metadata taxonomy_artifact = qiime2.Artifact.load('taxonomy.qza') taxonomy_md = taxonomy_artifact.view(qiime2.Metadata) taxa_tab, = metadata.visualizers.tabulate(input=taxonomy_md) ``` > [@samuel.drouin](#): > > Question 3 Still a bit light in this department (would welcome some contributions!): - [Artifact API — QIIME 2 2018.6.0 documentation](https://docs.qiime2.org/2018.6/interfaces/artifact-api/) (sounds like you found this already) - [Moving Pictures Python API tutorial (QIIME2 2018.4)](https://forum.qiime2.org/t/moving-pictures-python-api-tutorial-qiime2-2018-4/4112) (thanks @tomasz!) Hope that helps! :qiime2: 🦖 ---
**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [July 24, 2018, 1:52pm UTC](https://forum.qiime2.org/t/open-featuredata-in-artifact-api/5202/4 "2018-07-24T13:52:56Z")
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**Author:** ![samuel.drouin](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/s/f17d59/32.png) [@samuel.drouin](https://forum.qiime2.org/u/samuel.drouin)\ **Post date:** [July 25, 2018, 12:31am UTC](https://forum.qiime2.org/t/open-featuredata-in-artifact-api/5202/5 "2018-07-25T00:31:46Z")
Thank you for your help @thermokarst ! This is exactly what I was looking for. I would like to contribute to the Python API documentation in some way and will probably write some documentation about what I found out while writing the script. ---
**Author:** ![samuel.drouin](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/s/f17d59/32.png) [@samuel.drouin](https://forum.qiime2.org/u/samuel.drouin)\ **Post date:** [July 25, 2018, 2:49am UTC](https://forum.qiime2.org/t/open-featuredata-in-artifact-api/5202/6 "2018-07-25T02:49:16Z")
Is there any way to know what classes are accepted as view\_type for the artifact view function ? I tried the same thing on the DADA2 representative\_sequences : FeatureData[Sequences] and I get the following error : > rep\_seq.view(pandas.DataFrame) > Traceback (most recent call last): > File "", line 1, in > File "/Users/samueldrouin/conda/envs/qiime2/lib/python3.5/site-packages/qiime2/sdk/result.py", line 254, in view > return self.\_view(view\_type) > File "/Users/samueldrouin/conda/envs/qiime2/lib/python3.5/site-packages/qiime2/sdk/result.py", line 265, in \_view > recorder=recorder) > File "/Users/samueldrouin/conda/envs/qiime2/lib/python3.5/site-packages/qiime2/core/transform.py", line 59, in make\_transformation > (self.\_view\_type, other.\_view\_type)) > Exception: No transformation from \ to \ I am not sure what class I can use to get this class fasta file. I figured out that I can get the fasta file from the directory file structure but it most certainly is not the good way to do it : > rep\_seq.\_archiver.root\_dir > PosixPath('/var/folders/gh/9m466jhj1zn1jtk8w114w4dr0000gn/T/qiime2-archive-p\_4lnjwb/fda193f1-e60c-475b-a0a8-a1cb01f14925') ---
**Author:** ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)\ **Post date:** [July 25, 2018, 12:15pm UTC](https://forum.qiime2.org/t/open-featuredata-in-artifact-api/5202/7 "2018-07-25T12:15:43Z")
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**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [July 27, 2018, 12:46am UTC](https://forum.qiime2.org/t/open-featuredata-in-artifact-api/5202/8 "2018-07-27T00:46:46Z")
> [@samuel.drouin](#): > > I am not sure what class I can use to get this class fasta file. That is a great question @samuel.drouin! We really need to implement a convenience API for this, but in the meantime, you can do something like this to learn more about what you can directly transform to: ```python import qiime2 pm = qiime2.sdk.PluginManager() rep_seqs = qiime2.Artifact.load('/path/to/rep-seqs.qza') transform_to = pm.transformers[rep_seqs.format.file.format].keys() print('\n'.join([str(t) for t in transform_to])) ``` which returns: ```auto ``` Sorry for the inconvenience, hope that helps! 🦖 :qiime2: ---
**Author:** ![thermokarst](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@thermokarst](https://forum.qiime2.org/u/thermokarst)\ **Post date:** [July 27, 2018, 12:46am UTC](https://forum.qiime2.org/t/open-featuredata-in-artifact-api/5202/9 "2018-07-27T00:46:48Z")
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**Author:** ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)\ **Post date:** [August 27, 2018, 6:46am UTC](https://forum.qiime2.org/t/open-featuredata-in-artifact-api/5202/10 "2018-08-27T06:46:49Z")
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