new module: ANY2FASTA

Is there an existing module for this?

• I have searched for the existing module

Is there an open PR for this?

• I have searched for existing PRs

Is there an open issue for this?

• I have searched for existing issues

Further Information

This pkg is useful to allow for varied input formats (e.g., genbank and fasta, compressed and not), and automatically convert everything to plaintext fasta prior to analysis with another pkg that requires FastA inputs.

There's a bioconda recipe here and a corresponding container here.

Version print

any2fasta -v
yields
any2fasta 0.4.2

Help menu

any2fasta -h

Test

• note: this is from cwd of the github repo (tiny files are included for testing)

git clone git@github.com:tseemann/any2fasta.git
cd any2fasta
for ext in fq gbk gff; do
  any2fasta test.$ext > OUTPUT.$ext.fasta
done
du -sh OUTPUT.*.fasta
    # 300K        OUTPUT.fq.fasta
    # 4.5M        OUTPUT.gbk.fasta
    # 4.8M        OUTPUT.gff.fasta

Are you going to work on this?

• If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module