varsim 1.9.0

Generates all possible SNVs for MANE transcripts using HGVS nomenclature. Note: Not to be confused with the read simulator 'VarSim' (PMID: 25524895).

VarSim

Note on Naming: This tool, VarSim, is a sequence variant simulator for generating HGVS nomenclature. It is not affiliated with, and should not be confused with, the "VarSim" read simulator (PMID: 25524895).

VarSim generates simulations for all possible single nucleotide variants (SNVs) for the Matched Annotation from NCBI and EMBL-EBI (MANE) transcript, along with the corresponding protein using HGVS notation.

INSTALLATION

pip install varsim

CONFIGURATION (Mandatory)

Before you can use VarSim, you must set two environment variables to query the NCBI Entrez database.

EMAIL: (Required by NCBI) A valid email address so NCBI can contact you if there's an issue with your queries.

API_KEY: (Recommended) An NCBI API key, which allows for a much higher query rate. You can obtain one from your NCBI account settings.

Linux/macOS:

export EMAIL="[e-mail]"
export API_KEY="your_api_key_here"

Windows (PowerShell):

set EMAIL="[e-mail]"
set API_KEY="your_api_key_here"

USAGE

Variant Simulator

import varsim
# Assumes EMAIL and API_KEY are set
varsim.cds("INS")

[('NM_000207.3:c.1A>G', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.1A>T', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.1A>C', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.2T>G', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.2T>A', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.2T>C', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.3G>A', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.3G>T', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ('NM_000207.3:c.3G>C', 'NP_000198.1:p.(M1?)', 'NP_000198.1:p.(Met1?)'), ... ('NM_000207.3:c.328A>T', 'NP_000198.1:p.(N110Y)', 'NP_000198.1:p.(Asn110Tyr)'), ('NM_000207.3:c.328A>C', 'NP_000198.1:p.(N110H)', 'NP_000198.1:p.(Asn110His)'), ('NM_000207.3:c.329A>T', 'NP_000198.1:p.(N110I)', 'NP_000198.1:p.(Asn110Ile)'), ('NM_000207.3:c.329A>C', 'NP_000198.1:p.(N110T)', 'NP_000198.1:p.(Asn110Thr)'), ('NM_000207.3:c.330C>T', 'NP_000198.1:p.(N110=)', 'NP_000198.1:p.(Asn110=)'), ('NM_000207.3:c.330C>A', 'NP_000198.1:p.(N110=)', 'NP_000198.1:p.(Asn110=)'), ('NM_000207.3:c.330C>G', 'NP_000198.1:p.(N110=)', 'NP_000198.1:p.(Asn110=)')]

varsim.utr5("INS")

['NM_000207.3:c.-59A>G', 'NM_000207.3:c.-59A>T', 'NM_000207.3:c.-59A>C', 'NM_000207.3:c.-58G>A', 'NM_000207.3:c.-58G>T', ... 'NM_000207.3:c.-2C>A', 'NM_000207.3:c.-2C>T', 'NM_000207.3:c.-1C>G', 'NM_000207.3:c.-1C>A', 'NM_000207.3:c.-1C>T']

varsim.utr3("INS")

['NM_000207.3:c.*1A>G', 'NM_000207.3:c.*1A>T', 'NM_000207.3:c.*1A>C', 'NM_000207.3:c.*2C>G', 'NM_000207.3:c.*2C>A', ... 'NM_000207.3:c.*72G>T', 'NM_000207.3:c.*72G>C', 'NM_000207.3:c.*73C>G', 'NM_000207.3:c.*73C>A', 'NM_000207.3:c.*73C>T']

varsim.splice_site("INS")

['NC_000011.10(NM_000207.3):c.187+1G>A', 'NC_000011.10(NM_000207.3):c.187+1G>T', 'NC_000011.10(NM_000207.3):c.187+1G>C', 'NC_000011.10(NM_000207.3):c.187+2T>A', 'NC_000011.10(NM_000207.3):c.187+2T>G', 'NC_000011.10(NM_000207.3):c.187+2T>C', 'NC_000011.10(NM_000207.3):c.188-2A>G', 'NC_000011.10(NM_000207.3):c.188-2A>T', 'NC_000011.10(NM_000207.3):c.188-2A>C', 'NC_000011.10(NM_000207.3):c.188-1G>A', 'NC_000011.10(NM_000207.3):c.188-1G>T', 'NC_000011.10(NM_000207.3):c.188-1G>C']