How to extract FASTA representative sequences per biological sample from combined representative sequences (qzv) file?

[fgara]

Hi,

I have run my analysis for 35 samples together (35 samples in one metadata).
I now have a representative sequences (qzv) file that can be converted to FASTA sequences, but these include sequences for all samples, combined together.

How can I extract FASTA representative sequences (OTU / ASV sequences) per biological sample from this file?

I found the following:

Obtaining sequences per biological sample

Hello! I am wondering if there is a way I can obtain a list of the sequences PER biological sample. For example, rep-seqs and table.qzv as shown in the links below from the QIIME tutorials can give all the list of sequences but for all samples mixed together. Is there a way to get them per each biological (i.e.stool) sample per individual? https://view.qiime2.org/visualization/?type=html&src=https%3A%2F%2Fdocs.qiime2.org%2F2017.11%2Fdata%2Ftutorials%2Fmoving-pictures%2Frep-seqs.qzv https://…

But it's a long time ago, and the links it points to have changed.

Many thanks for your help and time

[jwdebelius (Justine Debelius)]

Hi @fgara,

it's slow (so possibly consider writing a for-loop) but check out qiime feature-table filter-seqs and then export (qiime tools export/qiime tools extract), which should give you the per-sample fasta files you want.

Best,
Justine

[fgara]

Hi Justine,

I was able to run the commands that you suggested, but I realized by default they exported the FASTA by creating a new directory, not as a file with the name I gave. So I tried the options given here:

Usage: qiime tools export [OPTIONS]

Exporting extracts (and optionally transforms) data stored inside an
Artifact or Visualization. Note that Visualizations cannot be transformed
with --output-format

Options:
--input-path ARTIFACT/VISUALIZATION
Path to file that should be exported [required]
--output-path PATH Path to file or directory where data should be
** exported to [required]**
--output-format TEXT Format which the data should be exported as. This
option cannot be used with Visualizations
--help Show this message and exit.

This command gives me an option to save output as file, but I couldn't get it work... I've tried it many times.

I also tried "fasta", ".fasta", ".txt" and so on for the option " --output-format ", but it also didn't work...

Can you help please?

Many thanks for your generous help

[jwdebelius (Justine Debelius)]

Hi @fgara,

You need to use DNAFASTAFormat as your output format. (I think this is linked to the input/output format tied to semantic types. You can also specify the sample name in the output path.

Best,
Justine