qiime2 plugin?

[mortonjt]

Would there be any interest in attaching a qiime2 plugin to this repository?

Of course, it would have to be resolved after merging #29
But it could be incredibly useful to have internal node relabeling in place; particularly for interpreting ILR coordinates.

[wasade]

Merged and yes, there would be a lot of interest to see a q2-plugin here

[mortonjt]

I was able to get t2t to work, even though it required a bit of massaging to convert from qiime2 taxonomy to a suitable taxonomy that t2t accepts. I can get a PR started in ~2 weeks.

[wasade]

Thanks! Q2 does not ensure all ranks are represented IIRC

…

On Apr 12, 2021, at 11:04 AM, Jamie Morton ***@***.***> wrote: I was able to get t2t to work, even though it required a bit of massaging to convert from qiime2 taxonomy to a suitable taxonomy that t2t accepts. I can get a PR started in ~2 weeks. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#31 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AADTZMTLVNFRTLSJNLDWEELTIMY4NANCNFSM42ZSJ7WA>.

[mortonjt]

Correct, I had to hack that in as well.
I had to use cat taxonomy.tsv | sed -e "1d" | cut -f1,2 > consistency.tsv followed by the following code to make q2 style taxonomy play nicely with t2t.

import pandas as pd
RANK_ORDER = ['d', 'p', 'c', 'o', 'f', 'g', 's']
taxa = pd.read_table('consistency.tsv', index_col=0, header=None)
def f(x):
    tabs = x.split('; ')
    n = len(RANK_ORDER) - len(tabs)
    if n > 0:
        return x + '; ' + '__; '.join(RANK_ORDER[-n:]) + '__'
    else:
        return x
data = taxa[1].apply(f)
data.to_csv('t2t_consistency.tsv', sep='\t', header=None)