"_input_with_circ.fasta" contains all sequences from input contigs.fasta

[jnesme]

When running viralverify, an output file "XXX_input_with_circ.fasta" is produced for input XXX.fasta.

However, this file contains the same number of sequences as the input. Exploring the repo, I noticed it should have been produced by check_circular.py.

I can't however manage to run that script solo, using a fresh install of ViralVerify: it throw an error first that fastaparser module is absent. I installed it with pip install fastaparser, and now the error is: AttributeError: module 'fastaparser' has no attribute 'read_fasta'

My question is : is it intended in viralverify workflow that XXX_input_with_circ.fasta be first a strict copy of the input fasta that is then trimmed to only "circs.fasta" based on annotation ? (HMM search is still running for me now).