Importing a compressed fasta file

Ideas and Suggestions
1

I’ve tried to qiime.Artifact.import_data a gzipped and zipped fasta file, and it doesn’t work. It is much more convenient to keep large fasta files zipped. Is there any way to import directly from a zip file?

Thank you!

2

Hey @BenKaehler,

When you say [quote=“BenKaehler, post:1, topic:211”]
import directly from a zip file
[/quote]

do you mean treating it like a directory? Or a single file that happens to be zipped?

For a single file, all we need is another format and some transformers. But if it’s the directory situation, it may not be that simple, we could probably treat it the same way, but there might be a more generic solution.

3

Thanks @ebolyen!

I mean a single zipped file, like fasta_file.fa.gz.

This would be handy for large reference files, but obviously it is more a nice-to-have sort of feature.

1 Like