I am currently using extract-reads plugin to play around with 16S sequences derived from whole genomes.
Using the CLI to extract the V4 region, I get the desired results
My CLI is as below and is pretty standard I would say.
qiime feature-classifier extract-reads
However using the API does not return any sequences.
Results (name = value)
reads = <artifact: FeatureData[Sequence] uuid: be200c8a-247a-4d51-bc3a-9c2f1ea413e2>
My command is below.
rep_seqs_v4 = extract_reads(sequences = rep_seqs,f_primer='GTGYCAGCMGCCGCGGTAA',r_primer='GGACTACNVGGGTWTCTAAT',read_orientation='forward')
I am not sure what is different?
I was careful that the rep_seqs would be the same in each instance.
I read in the fasta file using Artifact.import_data() and saved it out using rep_seqs.save('rep_seqs.qza')
So they should be the file in essence.