Hi @rnasrah,
Thanks for posting! I am not 100% sure what you are asking for, but @Mehrbod_Estaki might have provided your answer in point 2. Thanks @Mehrbod_Estaki for helping out!
The feature table is a matrix of sample X feature frequencies, so lists the abundance of each feature in each sample. I'm not sure if this is actually what you want, though, since you mention sequences specifically. (if @Mehrbod_Estaki is correct and this is what you want, follow his steps and then use biom convert -i feature-table.biom -o feature-table.tsv --to-tsv to convert to a text file that you can open in excel or a text reader).
Do you want a list of features (and corresponding sequences), similar to the rep-seqs file you posted, but for a single sample? In a future release this will be much more straightforward but for now you can get a FeatureData[Sequence] artifact containing sequences found in a single sample by following the steps in this post. That's a bit contrived and only contains sequences corresponding to a single sample, so I'm not sure if that's what you want to do (and it would be a laborious process if you want such a file for every sample you have).
If neither of these describe what you are looking for, could you please clarify with the following?:
- Write out a toy example, e.g., the first couple rows/columns of what your dream file should contain.
- Let us know what you want to do with this file. Even if QIIME2 does not yet output such a file, we may have an alternative approach if this file is an intermediate file in the approach you are attempting, or if it is input to another program.
I hope we can help!