Importing and Exporting Data into Qiime2

Import

You can import data into Qiime2 with the qiime tools import command. Let's assume that you have a protein FASTA file (my_data/my_proteins.fasta) and you want to import it into Qimme2 as a FeatureData[ProteinSequence] artifact. Run the following from my_data directory.

qiime tools import /
   --input-path my_data /
   --output-path my_proteis.qza /
   --type "FeatureData[ProteinSequence]"

This action will make sure that my_proteins.fasta is a valid proteins fasta file.

To get a list of all available formats run:

qiime tools list-types

Extract

To export data simply take the artifact name and use the qiime tools extract command. E.g.

qiime tools extract --input-path my_proteis.qza

This will create a folder named with a unique ID, within which your data is contained along with a bunch of metadata about the artifact.