ranks with full taxonomic hierarqui rather than featureid

[iratxezarra]

Hi

Is there a way to include the full hierarchical taxonomic names in the rank.qza file? ( rather than just the feature_id itself?) if i convert this rank file into qzv, then I visualize it in qiime view, and save them as .tsv I do not have a way to know which taxa they belong to...

thanks in advance

[mortonjt]

They are both metadata files, so it should be doable. You can definitely combine the taxonomy file with the metadata, but I don’t know of a qiime2 command that do this.

It’ll likely require something as follows in python

import qiime2 import pandas as pd taxa = qiime2.Artifact.load(“taxonomy.qza”).view(pd.DataFrame) ranks = qiime2.Artifact.load(“ranks.qza”).view(pd.DataFrame) combined = pd.concat((ranks.T, taxa), axis=1) combined.to_csv(“combined.txt”, sep=‘\t’)

In this way, you can view in excel, but it’ll be hard to sort the molecules ...

On Thu, Apr 22, 2021 at 7:33 AM iratxezarra @.***> wrote:

Hi

Is there a way to include the full hierarchical taxonomic names in the rank.qza file? ( rather than just the feature_id itself?) if i convert this rank file into qzv, then I visualize it in qiime view, and save them as .tsv I do not have a way to know which taxa they belong to...

thanks in advance

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[iratxezarra]

Great, Thanks so much. I will give it a try! :-) Iratxe Zarraonaindia Martinez Maria Goyri, Lab. 1.08. (Applied genomics and Bioinformatics) University of the Basque Country (UPV/EHU) Bº Sarriena s/n 48940, Leioa; Bilbao; Spain Tfno: +34-946015510 E-mail: @., @. http://www.genomic-resources.eu/

El jue, 22 abr 2021 a las 16:44, Jamie Morton @.***>) escribió:

They are both metadata files, so it should be doable. You can definitely combine the taxonomy file with the metadata, but I don’t know of a qiime2 command that do this.

It’ll likely require something as follows in python

import qiime2 import pandas as pd taxa = qiime2.Artifact.load(“taxonomy.qza”).view(pd.DataFrame) ranks = qiime2.Artifact.load(“ranks.qza”).view(pd.DataFrame) combined = pd.concat((ranks.T, taxa), axis=1) combined.to_csv(“combined.txt”, sep=‘\t’)

In this way, you can view in excel, but it’ll be hard to sort the molecules ...

On Thu, Apr 22, 2021 at 7:33 AM iratxezarra @.***> wrote:

Hi

Is there a way to include the full hierarchical taxonomic names in the rank.qza file? ( rather than just the feature_id itself?) if i convert this rank file into qzv, then I visualize it in qiime view, and save them as .tsv I do not have a way to know which taxa they belong to...

thanks in advance

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.

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