Countess-Variant-Caller

This is a variant caller which makes HGVS variant strings from DNA sequences. It it part of the CountESS Project but may be used separately.

It is intended to be fast and efficient when finding a small variation from a known sequence, as is common in mutational scanning experiments.

Typical usage calling DNA changes:

>>> from countess_variant_caller import find_variant_string

>>> find_variant_string("g.", "GATTACA", "GTTTACA")
'g.2A>T'

>>> find_variant_string("g.", "GATTACA", "GTTCAGA")
'g.[2A>T;4T>C;6C>G]'

It also does protein variant calling:

>>> from countess_variant_caller import find_variant_string

>>> find_variant_string("p.", "ATGGTTGGTTCA", "ATGGTTGGTGGTTCA")
'p.Gly3dup'

>>> find_variant_string("p.", "ATGGTTGGTTCA", "ATGGCTGCTTCA")
'p.Val2_Gly3delinsAlaAla'

Contributors

• Nick Moore nick@zoic.org.

License

Copyright (C) 2022- CountESS Developers under BSD 3-Clause license, see LICENSE.txt.