flasc

inFLuenza Amino acid Substitution Caller

Usage

--all mode (default)

Displays every scanned site, including invariant ones

./mutation_scan.py -i HA.aligned.faa -d mutations.toml -t "HA" -q  UJS29065.1 --mode all

query   gene    coordinate      variant reference       residue note
UJS29065.1      HA      170     N158D   N       N       H3 numbering; mammalian adaptation
UJS29065.1      HA      172     T160A   T       A       H3 numbering; mammalian adaptation
UJS29065.1      HA      198     N186K   N       N       H3 numbering; synonym: N182K; mammalian adaptation (enhanced binding to alpha-2,6 SA)
UJS29065.1      HA      208     Q196R   Q       K       H3 numbering; synonym: Q192R (H5 numbering); mammalian adaptation (enhanced binding to alpha-2,6 SA)
UJS29065.1      HA      236     N224K   N       N       H3 numbering; mammalian adaptation
UJS29065.1      HA      205     K193R   K       N       H3 numbering; synonym: K189R (H5 numbering); mammalian adaptation
UJS29065.1      HA      238     Q226L   Q       Q       H3 numbering; synonym: Q222L (H5 numbering); mammalian adaptation
UJS29065.1      HA      240     G228S   G       G       H3 numbering; mammalian adaptation
UJS29065.1      HA      331     T318I   T       T       H3 numbering; mammalian adaptation

--variants mode

Displays the line if the query sequence is different from the reference, even if the residue does not match that of the definition

./mutation_scan.py -i HA.aligned.faa -d mutations.toml -t "HA" -q  UJS29065.1 --mode variants

query   gene    coordinate      variant reference       residue note
UJS29065.1      HA      172     T160A   T       A       H3 numbering; mammalian adaptation
UJS29065.1      HA      208     Q196R   Q       K       H3 numbering; synonym: Q192R (H5 numbering); mammalian adaptation (enhanced binding to alpha-2,6 SA)
UJS29065.1      HA      205     K193R   K       N       H3 numbering; synonym: K189R (H5 numbering); mammalian adaptation

./mutation_scan.py -i HA.aligned.faa -d mutations.toml -t "HA" -q  UJS29065.1 --mode strict

--strict mode

Displays only the variants that exactly match the predefined substituion(s)

query   gene    coordinate      variant reference       residue note
UJS29065.1      HA      172     T160A   T       A       H3 numbering; mammalian adaptation

Output table

query gene coordinate variant_id ref alt note

Col	Type	Description
1	string	Query sequence name
2	string	Query gene name
3	int	Query coordinate (1-based; closed)
4	string	Variant ID
5	string	Reference (wildtype) residue
6	string	Query residue
7	string	Notes (numbering scheme, synonyms, effects etc.)

Variant definition file

The variants are defined in a TOML format table

[PB2]
[PB2.E627K]
name = "E627K"
protein_id = "YP_308664.1"
gene_id = "PB2"
subtypes = "all"
wildtype = "E"
mutant = "K"
coordinate = "627"
reference_isolate = "A/goose/Guangdong/1/1996(H5N1)"
note = "mammalian adaptation"
citations = ["https://doi.org/10.1126/science.1062882",
            "https://doi.org/10.1128/jvi.67.4.1761-1764.1993"]
[PB2.D701N]
name = "D701N"
protein_id = "YP_308664.1"
gene_id = "PB2"
subtypes = "all"
wildtype = "D"
mutant = "N"
coordinate = "701"
reference_isolate = "A/goose/Guangdong/1/1996(H5N1)"
note = "mammalian adaptation"

# continued