//hgvs example: LRG_199p1:p.(Met1?)
public void StartLost_due_to_substitution()
{
Assert.Equal("LRG_199p1:p.(Met1?)", HgvspNotation.GetSubstitutionNotation("LRG_199p1", 1, "Met", "Cys"));
}
public void Stop_lost_without_countToEnd()
{
Assert.Equal("NP_001263627.1:p.(Ter327ArgextTer?)", HgvspNotation.GetExtensionNotation("NP_001263627.1", 327, "Ter", "Arg", -1));
}
//hgvs example: NP_003997.1:p.Cys188=
public void Silent_substitution()
{
Assert.Equal("NP_003997.1:c.XXX(p.(Cys188=))", HgvspNotation.GetSilentNotation("NP_003997.1:c.XXX", 188, "Cys", false));
}
//NP_001263627.1:p.(Met1?)
public void Start_lost_start_not_equals_end()
{
Assert.Equal("NP_001263627.1:p.?", HgvspNotation.GetStartLostNotation("NP_001263627.1"));
}
// from varnom: p.Ter110Glnext*17
public void Stop_lost_with_countToEnd()
{
Assert.Equal("NP_001263627.1:p.(Ter110GlnextTer17)", HgvspNotation.GetExtensionNotation("NP_001263627.1", 110, "Ter", "Gln", 17));
}
//p.Trp26Ter
public void Deletion_gained_stop()
{
Assert.Equal("NP_003997.1:p.(Trp26Ter)", HgvspNotation.GetDeletionNotation("NP_003997.1", 26, 27, "Trp", true));
}
// hgvs example:NP_003997.1:p.(Lys2_Gly3insGlnSerLys)
public void Insertion_at_end()
{
Assert.Equal("NP_003997.1:p.(Cys6_Ter7insGlnSerLys)", HgvspNotation.GetInsertionNotation("NP_003997.1", 6, 7, "GlnSerLys", "MKGABC*"));
}
// hgvs example:NP_003997.1:p.(Tyr4Ter)
public void Frameshift_gains_immediate_stop()
{
Assert.Equal("NP_003997.1:p.(Tyr4Ter)", HgvspNotation.GetFrameshiftNotation("NP_003997.1", 4, "Tyr", "TerCysIle", -1));
}
// hgvs example:NP_003997.1:p.(Ile327ArgfsTer?)
public void Frameshift_unknown_countToStop()
{
Assert.Equal("NP_003997.1:p.(Ile327ArgfsTer?)", HgvspNotation.GetFrameshiftNotation("NP_003997.1", 327, "Ile", "Arg", -1));
}
//Pro578_Lys579 goes to TerLeu
public void Delins_becomes_substitution_of_Ter()
{
Assert.Equal("NP_003997.1:p.(Pro578Ter)", HgvspNotation.GetDelInsNotation("NP_003997.1", 578, 579, "ProLys", "TerLeu"));
}
// hgvs example:NP_003997.1:p.(Arg97ProfsTer23)
public void Frameshift_with_known_countToStop()
{
Assert.Equal("NP_003997.1:p.(Arg97ProfsTer23)", HgvspNotation.GetFrameshiftNotation("NP_003997.1", 97, "Arg", "Pro", 23));
}
// hgvs example:NP_003997.1:p.(Pro578_Lys579delinsLeuTer)
public void Del_two_ins_stop()
{
Assert.Equal("NP_003997.1:p.(Pro578_Lys579delinsLeuTer)", HgvspNotation.GetDelInsNotation("NP_003997.1", 578, 579, "ProLys", "LeuTer"));
}
// hgvs example:NP_003997.1:p.(Cys28_Lys29delinsTrp)
public void Del_two_ins_one()
{
Assert.Equal("NP_003997.1:p.(Cys28_Lys29delinsTrp)", HgvspNotation.GetDelInsNotation("NP_003997.1", 28, 29, "CysLys", "Trp"));
}
// hgvs example:NP_003997.1:p.(Cys28delinsTrpVal)
public void Del_one_ins_two()
{
Assert.Equal("NP_003997.1:p.(Cys28delinsTrpVal)", HgvspNotation.GetDelInsNotation("NP_003997.1", 28, 28, "Cys", "TrpVal"));
}
// hgvs example:NP_003997.1:p.(Ala3del)
public void One_aminoAcid_deletion()
{
Assert.Equal("NP_003997.1:p.(Ala3del)", HgvspNotation.GetDeletionNotation("NP_003997.1", 3, 3, "Ala", false));
}
//hgvs example: LRG_199p1:p.Trp24Ter
public void Nonsense_substitution()
{
Assert.Equal("LRG_199p1:p.(Trp24Ter)", HgvspNotation.GetSubstitutionNotation("LRG_199p1", 24, "Trp", "Ter"));
}
// hgvs example:NP_003997.1:p.(Ala3_Ser5del)
public void Multiple_aminoAcid_deletion()
{
Assert.Equal("NP_003997.1:p.(Ala3_Ser5del)", HgvspNotation.GetDeletionNotation("NP_003997.1", 3, 5, "AlaLysSer", false));
}
public void Frameshift_due_to_insertion()
{
Assert.Equal("NP_003997.1:p.(Cys3ArgfsTer40)", HgvspNotation.GetFrameshiftNotation("NP_003997.1", 3, "Cys", "Arg", 40));
}
public void Unknown_start_equals_end()
{
Assert.Equal("NP_003997.1:p.(Arg26Cys)", HgvspNotation.GetUnknownNotation("NP_003997.1", 26, 26, "Arg", "Cys"));
}
// hgvs example:NP_003997.1:p.(Lys2_Gly3insGlnSerLys)
public void Multiple_aminoAcid_insertion()
{
Assert.Equal("NP_003997.1:p.(Lys2_Gly3insGlnSerLys)", HgvspNotation.GetInsertionNotation("NP_003997.1", 2, 3, "GlnSerLys", "MKGABC"));
}
