serious constellations of reoccurring phylogenetically-independent origin

1. classify - takes a set of lineage-defining constellations with rules and classifies sequences by them.
2. haplotype - takes a set of constellations and writes haplotypes (either as strings or individual columns).
3. report - creates a report HTML for a constellation
4. define - takes a CSV with a group column and a mutations column and extracts the common mutations within the group, optionally with reference to a specified outgroup

• -i, --input - primary input file (usually the FASTA file)
• -m, --metadata - the metadata CSV file (required for some commands)
• -o, --output - the output file or path
• -p, --prefix - the output prefix (when multiple output files are being produced)
• -c, --constellation - a file of one or more constellations in JSON format (default to installed file from constellation github?)
• -n, --names - a list of constellation names to include from the file

The JSON file for an individual constellation (in this case a lineage defining one) would look like this:

{
	"name": "B.1.1.7",
	"description": "B.1.1.7 lineage defining mutations",
	"citation": "https://virological.org/t/563",
	"sites": [
		"nuc:C913T",
		"1ab:T1001I",
		"1ab:A1708D",
		"nuc:C5986T",
		"1ab:I2230T",
		"1ab:SGF3675-",
		"nuc:C14676T",
		"nuc:C15279T",
		"nuc:C16176T",
		"s:HV69-",
		"s:Y144-",
		"s:N501Y",
		"s:A570D",
		"s:P681H",
		"s:T716I",
		"s:S982A",
		"s:D1118H",
		"nuc:T26801C",
		"8:Q27*",
		"8:R52I",
		"8:Y73C",
		"N:D3L",
		"N:S235F"
	],
        "rules": {
                "min_alt": 4,
                "max_ref": 6,
        }
}

The general format of a mutation code is: gene:[ref]coordinates[alt] where gene is a gene code (or nuc for the genomic nucleotide sequence), ref is the nucleotide or amino acids in the reference, alt is the specific nucleotide or amino acid for the mutatant. Either of ref or alt can be missing if no specific state is required.

Rules can either specify [min|max]_[ref|alt|ambig|oth] OR the call required at a mutation e.g. "N:S235F": (not )[ref|alt|ambig|oth]

The following are valid ways to describe variants of each type. We prefer the definition at the top of each list, but provide alternatives for backwards compatibility.

• these are case insensitive e.g. S vs s
• genes can be full e.g. orf1ab spike, or shortened e.g. 1ab, s
• protein based definitions may be acceptable if the reference JSON includes them but may not be shortened e.g. NSP2
• all coordinates are 1-based
• for amino acid mutations, reference can be longer than 1 amino acid

SNP:

• nuc:[ref]nucleotide_coordinate[alt]
• snp:[ref]nucleotide_coordinate[alt]

Amino acid mutation:

• gene:[ref]amino_acid_coordinate_relative_to_gene[alt]
• protein:[ref]amino_acid_coordinate_relative_to_protein[alt]
• gene:[ref]amino_acid_coordinate_relative_to_gene - this allows any other aa to be called as alt
• aa:gene:[ref]amino_acid_coordinate_relative_to_gene[alt]
• aa:protein:[ref]amino_acid_coordinate_relative_to_protein[alt]
• aa:gene:[ref]amino_acid_coordinate_relative_to_gene - this allows any other aa to be called as alt

Deletion:

• del:nucleotide_coordinate:nucleotide_length
• gene:[ref]amino_acid_coordinate-
• gene:[ref]amino_acid_coordinatedel

Insertion (currently parsed but not typed):

• nuc:nucleotide_coordinate+inserted_sequence
• snp:nucleotide_coordinate+inserted_sequence
• gene:amino_acid_coordinate_relative_to_gene+inserted_sequence
• aa:gene:amino_acid_coordinate_relative_to_gene+inserted_sequence