public void CustomAnnotationForIndel2()
{
JsonUtilities.CustomAlleleContains("chr3 1363515 . TA T . . .", null,
new List <string> {
Resources.CustomAnnotations("chr3_1363515_1363516_hgmd.nsa")
},
"NM_014461.3:c.944delA");
}
public void CustomAnnotationForSnv()
{
JsonUtilities.CustomAlleleContains("chr1 11893 . T G . . .", null,
new List <string> {
Resources.CustomAnnotations("chr1_11893_13957_internalAF.nsa")
},
"InternalAF");
}
public void OutputBasicCustomAnnotation()
{
JsonUtilities.CustomAlleleContains("chr1 949523 . C T . . CLASS=DM",
null,
new List <string> {
Resources.CustomAnnotations("chr1_949523_949524_hgmd.nsa")
},
"\"HGMD\":[{\"altAllele\":\"T\",\"isAlleleSpecific\":true,\"mutationCategory\":\"DM\",\"mutantAllele\":\"ALT\",\"gene\":\"ISG15\",\"strand\":\"+\",\"hgvsCoding\":\"NM_005101.3:c.163C>T\",\"hgvsProtein\":\"NP_005092.1:p.Q55*\",\"phenotype\":\"Idiopathic_basal_ganglia_calcification\",\"hgmdAccession\":\"CM1411641\"}]");
}
public void RegularAndCustomAnnotation()
{
JsonUtilities.CustomAlleleContains(
"chr1 985955 . G C . . CLASS=DM;MUT=ALT;GENE=AGRN;STRAND=+;DNA=NM_198576.3:c.5125G>C;PROT=NP_940978.2:p.G1709R;DB=rs199476396;PHEN=Myasthenia;ACC=CM094737",
Resources.MiniSuppAnnot("chr1_985955_985956.nsa"),
new List <string> {
Resources.CustomAnnotations("chr1_985955_985955_hgmd.nsa")
},
"{\"altAllele\":\"C\",\"refAllele\":\"G\",\"begin\":985955,\"chromosome\":\"chr1\",\"dbsnp\":[\"rs199476396\"],\"end\":985955,\"variantType\":\"SNV\",\"vid\":\"1:985955:C\",\"clinVar\":[{\"id\":\"RCV000019902.29\",\"reviewStatus\":\"no assertion criteria provided\",\"isAlleleSpecific\":true,\"alleleOrigins\":[\"germline\"],\"refAllele\":\"G\",\"altAllele\":\"C\",\"phenotypes\":[\"Myasthenic syndrome, congenital, 8\"],\"medGenIDs\":[\"C3808739\"],\"omimIDs\":[\"615120\"],\"orphanetIDs\":[\"590\"],\"significance\":\"pathogenic\",\"lastUpdatedDate\":\"2016-08-29\",\"pubMedIds\":[\"19631309\"]},{\"id\":\"RCV000235029.1\",\"reviewStatus\":\"no assertion criteria provided\",\"isAlleleSpecific\":true,\"alleleOrigins\":[\"germline\"],\"refAllele\":\"G\",\"altAllele\":\"C\",\"phenotypes\":[\"Congenital myasthenic syndrome\"],\"medGenIDs\":[\"C0751882\"],\"significance\":\"pathogenic\",\"lastUpdatedDate\":\"2016-08-29\",\"pubMedIds\":[\"19631309\"]}],\"HGMD\":[{\"altAllele\":\"C\",\"isAlleleSpecific\":true,\"mutationCategory\":\"DM\",\"mutantAllele\":\"ALT\",\"gene\":\"AGRN\",\"strand\":\"+\",\"hgvsCoding\":\"NM_198576.3:c.5125G>C\",\"hgvsProtein\":\"NP_940978.2:p.G1709R\",\"dbsnp137\":\"rs199476396\",\"phenotype\":\"Myasthenia\",\"hgmdAccession\":\"CM094737\"}]}");
}
public void CustomAnnotationForRefMinor()
{
JsonUtilities.CustomAlleleContains(
"chr1 1269554 . T . . . .",
Resources.MiniSuppAnnot("chr1_1269554_1269554.nsa"),
new List <string> {
Resources.CustomAnnotations("chr1_1269554_1269554_hgmd.nsa"), Resources.CustomAnnotations("chr1_1269554_1269554_internalAF.nsa")
},
"HGMD");
JsonUtilities.CustomAlleleDoesNotContains(
"chr1 1269554 . T . . . .",
Resources.MiniSuppAnnot("chr1_1269554_1269554.nsa"),
new List <string> {
Resources.CustomAnnotations("chr1_1269554_1269554_hgmd.nsa"), Resources.CustomAnnotations("chr1_1269554_1269554_internalAF.nsa")
},
"InternalAF");
}
public void MultipleRealCustomAnnotations()
{
JsonUtilities.CustomAlleleContains(
"chr1 957605 . G A . . CLASS=DM;MUT=ALT;GENE=AGRN;STRAND=+;DNA=NM_198576.3:c.5125G>C;PROT=NP_940978.2:p.G1709R;DB=rs199476396;PHEN=Myasthenia;ACC=CM094737",
null,
new List <string> {
Resources.CustomAnnotations("chr1_957605_957605_hgmd.nsa"), Resources.CustomAnnotations("chr1_957605_957605_internalAF.nsa")
},
"HGMD");
JsonUtilities.CustomAlleleContains(
"chr1 957605 . G A . . CLASS=DM;MUT=ALT;GENE=AGRN;STRAND=+;DNA=NM_198576.3:c.5125G>C;PROT=NP_940978.2:p.G1709R;DB=rs199476396;PHEN=Myasthenia;ACC=CM094737",
null,
new List <string> {
Resources.CustomAnnotations("chr1_957605_957605_hgmd.nsa"), Resources.CustomAnnotations("chr1_957605_957605_internalAF.nsa")
},
"InternalAF");
}
public void AlleleSpecificForInternalAF()
{
JsonUtilities.CustomAlleleContains(
"chr1 1269554 . T C . . .",
Resources.MiniSuppAnnot("chr1_1269554_1269554.nsa"),
new List <string> {
Resources.CustomAnnotations("chr1_1269554_1269554_hgmd.nsa"), Resources.CustomAnnotations("chr1_1269554_1269554_internalAF.nsa")
},
"HGMD");
JsonUtilities.CustomAlleleContains(
"chr1 1269554 . T C . . .",
Resources.MiniSuppAnnot("chr1_1269554_1269554.nsa"),
new List <string> {
Resources.CustomAnnotations("chr1_1269554_1269554_hgmd.nsa"), Resources.CustomAnnotations("chr1_1269554_1269554_internalAF.nsa")
},
"InternalAF");
}
