This function reconstructs insertions on each branch in RSV phylogenetic trees, compares them to deletions and outputs a CSV file comparing insertions and deletions.

The function inputs include:

• genbank format genome reference

• annotated tree (json format)

• tree (nwk format)

• insertion file (csv format)

• aligned G amino acid file (fasta)

The reference files are available in the data/ folder. The rest of the inputs can be generated by running the without_G_workflow

The output consists of a TSV file with columns for insertion and deletion length and location in the G gene.

This function can be run manually the command line as:

	python3 insertions_and_deletions.py \

	--tree {tree file nwk format} \

	--json {annotated tree json format} \

	--reference {annotated genome reference gbk format} \

	--insertions {insertions file CSV format} \
	
	--alignedgene {aligned G amino acid file} \

	--output {output file TSV format}

It can also be run using Snakemake with

	snakemake --cores all