ID	REF	ALT	SEQ	FLANK	REF_dG	REF_ED	ALT_dG	ALT_ED	SNPfold_score	RNAsnp_score	RipRap_score	RemuRNA_score
ID2	C	G	TAACACACACGTGCTTACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTCACTTGTATACTGATTTTACGTACGCACACGGATGCTACAGTA	51	-6.60	19.53	-7.30	25.05	0.867172	Error	26.873	2.651
ID2	U	G	AACACACACGTGCTTACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTCACTTGTATACTGATTTTACGTACGCACACGGATGCTACAGTATAACACACACGTGCTTACCCTACCACTTTATACCACCACCACATGCCATACTCACCCTCACTTGTATACTGATTTTACGTACGCACACGGATGCTACAGTA	101	-18.00	45.05	-20.60	31.59	0.926023	0.4816	4.995	2.931


cwd=$(pwd)
variantfoldrna run \
    --ref-genome=${cwd}/example_input/yeast_ref_genome.fa  \
    --gff=${cwd}/example_input/yeast_gene_model.gff3 \
    --vcf=${cwd}/example_input/saccharomyces_cerevisiae_subset.vcf \
    --flank-len=50 \
    --ribosnitch-prediction-tool=SNPfold,Riprap,rnasnp:p-value \
    --tmp-dir=${cwd}/tmp_yeast \
    --out-dir=${cwd}/yeast_ribosnitches \
    --canonical \
    --spliced --use-conda --conda-frontend=mamba --conda-prefix=~/scratch/conda_envs