public void With_rnaEdits_reverse_deletion_utr()
{
//NM_001317107.1 chr14:22138125-22139232
var genomicSeq = new SimpleSequence("ATATGGTATGTAACTTATTCTTTGCAAGGCGCTTCTTTAATTTGGAGCACCACGTATCCTAAGGACGTAGACATTTTCATTTTTCTTCTTTTCTCTCTTTTCTCCCCACTAACTTGTTTAAGGCACTCTTCATTTCTTCATTCCTAAGGGTATAGATAATGGGGTTCAGCAGGGGGGTGACTGCAGTGAAAAACACAGATACTGCCTTGTCCTCTGGGAGGCTGGTGGATGGGCGGGAATAGATGAAGATGCAGTGTCCCAGGAACAGTGTAACTACAGTGAGATGGGCTGCACAGGTGGACAGGGCCTTCCACTTGCCCTTGGAGATCTGCTGCCTCAGACTCACCAGGATGACTGCGTAGGACACCACCAGGACCACAAAACAGACCACGGAGATCAATCCACTGTTGGAGACAATGAGGATCTCAAGGACGTGGGTGTGTCAATGCAGGCCAGCTTGATCACCTGAGGTACATCACAGAAGAAGTTGTCAATCTCATCAGGACCACAGTAGGGCAGCTTGATGGTAAGGGAGGTGAGGGCTATGGAGTGGATGGTCCCTCCTGTCCAGAGGGCCACAGCCAGCAGCACACATACCTTCCAGTTCATCACTATCATGTACTGCAGGGGTTTACAGATGGCCACATACCGATCATAGGCCATGACGGTGAGGAGGAAGATCTCTGTGCAGGCAAAGAGGTGCAGGAAGAACATCTGGGTCACACAGGCATCAAAAGAGATGAGCTTTTCCTCTGACCACACGTCTCTCAGCATCTTGGGGACAGTGACAGTGGAGTGGCAGACATCAATAAAGGACAGGTTGCTGAGGAAGAAATACATGGGAGTATGGAGCCGGTGGTCATAGATAATAGTTATGACAATGAGAACATTCCCAATCAGTGTCAGGACATAAAAAATGAGGAACATGGAAAACATAGCTATCCGTGCCTTATGATTTACAGATAAACCTCTAAGCCGAAAATATGTCACTAAAGAAGTTTGATTGAGTAGGATGGCCTCTTCCATTCTCTTTGTTAGACAACCTGTAAAGAATTAGAAAAAAAGTCTAATATAACACAGTATCTGCATCAATCATTTGGTCATTTAA", 22138125 - 1);
var codingRegion = new CodingRegion(22138201, 22139150, 83, 1030, 948);
var regions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 1, 22138125, 22138561, 670, 1106),
new TranscriptRegion(TranscriptRegionType.Gap, 1, 22138562, 22138563, 669, 670),
new TranscriptRegion(TranscriptRegionType.Exon, 1, 22138564, 22139232, 1, 669)
};
var rnaEdits = new IRnaEdit[]
{
new RnaEdit(905, 905, "T"),
new RnaEdit(796, 796, "C"),
new RnaEdit(679, 679, "A"),
new RnaEdit(670, 671, "")
};
const byte startExonPhase = 0;
var codingSequence = new CdnaSequence(genomicSeq, codingRegion, regions, true, rnaEdits);
var expectedCodingSeq = "ATGGAAGAGGCCATCCTACTCAATCAAACTTCTTTAGTGACATATTTTCGGCTTAGAGGTTTATCTGTAAATCATAAGGCACGGATAGCTATGTTTTCCATGTTCCTCATTTTTTATGTCCTGACACTGATTGGGAATGTTCTCATTGTCATAACTATTATCTATGACCACCGGCTCCATACTCCCATGTATTTCTTCCTCAGCAACCTGTCCTTTATTGATGTCTGCCACTCCACTGTCACTGTCCCCAAGATGCTGAGAGACGTGTGGTCAGAGGAAAAGCTCATCTCTTTTGATGCCTGTGTGACCCAGATGTTCTTCCTGCACCTCTTTGCCTGCACAGAGATCTTCCTCCTCACCGTCATGGCCTATGATCGGTATGTGGCCATCTGTAAACCCCTGCAGTACATGATAGTGATGAACTGGAAGGTATGTGTGCTGCTGGCTGTGGCCCTCTGGACAGGAGGGACCATCCACTCCATAGCCCTCACCTCCCTTACCATCAAGCTGCCCTACTGTGGTCCTGATGAGATTGACAACTTCTTCTGTGATGTACCTCAGGTGATCAAGCTGGCCTGCATTGACACCCACGTCATTGAGATCCTCATTGTCTCCAACAGTGGATTGATCTCCGTGGTCTGTTTTGTGGTCCTGGTGGTGTCCTACGCAGTCATCCTGGTGAGTCTGAGGCAGCAGATCTCCAAGGGCAAGCGGAAGGCCCTGTCCACCTGTGCAGCCCATCTCACTGTAGTTACACTGTTCCTGGGACACTGCATCTTCATCTATTCCCGCCCATCCACCAGCCTCCCAGAGGACAAGGTAGTATCTGTGTTTTTCACTGCAGTCACCCCCCTGCTGAACCCCATTATCTATACCCTTAGGAATGAAGAAATGAAGAGTGCCTTAAACAAGTTAGTGGGGAGAAAAGAGAGAAAAGAAGAAAAATGA";
Assert.Equal(expectedCodingSeq, codingSequence.GetCdnaSequence().Substring(codingRegion.CdnaStart - 1, codingRegion.Length));
}
public void RnaEdits_in_coding_sequence_reverse_insertion()
{
//NM_000682.6, chrom: chr2:96778623-96781984
var genomicSeq = new SimpleSequence("CTTATTACAAAATATCCTTTATTGATAAAATAGCTCAGAGTTTAAAAAAAAAAAAAACACCACCTGCATGTCGCAATAAGAGGTCACAGGCAAGAACACTGGGGGTCCCATGGGGCGCACACAAGACCGGCCAGCAGAGGGTCACAGTCAGTCCCTCTCCTGGCCCAGCTCCCCACCACATCCCAGGGCGATACTCTGGCCTCAACAACCCACTGAGGACCAAGCTGGGAAGCCTCCCACACCCCAGGAAGGACTCTTTTTGGTCCCCTCCATTCTCTCTACACCCAGAAAACTCCCTCGGTGCCCTTCCAAATCTAGCAGGTCCATCTGGCCCATTCCCCCGACACCTGCCAAGCTAAGATGCCTACTGGCCCAATGTTGAAGCCAGGCCCTCTCCAAGGGAAGGCCGATAAACCTCCTTTCCACACTTCCAACTGTTCTGGGTGCCAGGTTTTGGGGTGGGACTGAGAACCAGGAAGCAGGGGTCCTCAATGCACAGCCCCATCAGCATTGCGGGGAGCAGCGTGGCTGGGTCCGAGGCAGTCCACAAGCACCCACCTGGGGGGATCAGTTGTGGTTCACAAGGACTCATTTGGGGCTTGGAGACCTGGCCGGGCACTCCAGTGGGAGGCTCCCCTAGGGGCGCACCAGGCTCTGATGCCAGTACCCCACCTGGGGGCGCTGCCACCTGTCACAGGCTCTCATCTTAGACTGTTGCCGAGGTGTGGATATTTTGAGCTGTCTTGGGGAGACAATTTGCCTCCTTGATGACAAAAGACTTATCCCCCACTGGGGAGACCCAAGCCACTAAAAACCCTCTTGGTGTTGCCGGTGAAATGTCGAAACGTTGTCATGTAGCGTAATAACTCAGACCTTTGCAGCCAGAAGAACACATTCTCAAAGAGATCCTTTAACTTGAAATAGTGATTCTGTCTGCCACTCCCGGCTTCCAGTTCGGGGTAGGAATTCACACACCCCAGGGACAGAACAAAAGTCTACAGGAAGACAGGTGGTGGTAAACACAGAGGAAAGGGATTTTTATATCACCATATAATCACATTTTTGGTTCTCTAGTGTGTTCCCCCACAGAGCTCAAAGCTTTCTGCAAAGCCTTTCATCTCCCTGCAGCAAGTAGGCAGTGAGCTATTGTCGCCCCGATTTTTGCAGGGGGTGAATGCCAGTGATCGGGGATCTCCCGTCGAGGCAGAGACCAGGCCTCCAAGACCGCCCCAGCGAGGCATCCACGTGGCCACCCACCTACCGGAGGGGTGCTGGGTAAGGAAGCCGATCCATTGTTCTGGCTTTCAAAGGAACCACAGATCCGAAAACAGGCAAAGGGGGAAAGGAGGGCCCAGAGACGATGCCACCCCATAAGCCCCCATCCCAGCGCCTGCCAGGGACCGCGAGTGCCTAGCGTGGGTGATCAGTCTTCGTTTCTTCCTCCCCCTCAGCAGCAGGCCCCACTGGGAAAAGTGGAAGGCTGGCTCCGTGCTCTTTGTGGGTGGGGGGGAGATGAAAAAGAAACGAAAACACCACAAGCAAGTGACCTGCCAGGAACACAAGGTCCTCAAGAAAGGGAAGCCCAGACATTGGTCTGGAGAGCATGGGGCTCTGGGAAGAAAGTGCTCTCTCTTCTCCTGGTCTTGGCTATGTTCCAGAGGATTTGAACCACCTCCATCGGCCTGTGCTCAGGGAGAGGGTGGAGAAGGGGTCCCCCACAGCTAAGCCGGCAAGGGGAAGCTTCACTGGGACCCTTGCTAGCAGCCCCCCTGCCCACCCCTCCCAAGGGGTTCCTAAGATGAGGCCTACAGGATCTGGGCAGGGAGCAGAAAGCCCAGGGGAGGCAGCCACACACAGCAGGGCAAGAAGCAGGGTGACCCCGGCGCCACCGCACCAACCCCACAGGGGCAGCGCAGGCGGGCTCACCAGGCCGTCTGGGTCCACGGGCGGCACAGGATCCTCCGGAAGGCACGGCGGAAGTCCTGGTTGAAGATGGTGTAGATAACAGGGTTCAGTGAGCTGTTGCAGTAGCCGATCCAGAAGAAGAACTGGAAGAGGCCATGGGGCACCTTGCAGTGCTTCGGGCAGATGGCTCCCAGGCTGTAGCTGAAGAAGAAGGGGAACCAGCAGAGCACAAAAACGCCAATGACCACAGCCAGCACGAAGGTGAAGCGCTTCTCCCGGGTCAGCTGCGCCCGTCGACGCCACCACTGCCCACCTATAGCACCCACGCCCCTGCCCAGGAGCACCTGGCCACGTAGGGTGGCCAGCACCCGGGAGCCCTGTGGCTGCTGCAGCGGGGGGCTGCAAGCTGAGGCCGGAGACACTGGCACTGCCTGGGGTTCACACTCTTCCTCCTCCTCCTCCTCCTCTTCAGCTTCATCCTCTGGAGATGCCCCACAAACACCCTCCTTCTGGCCCTGGCCTGAGTTGGGAAGGGCAGCCCAACTGGGTGGCAAGGCCCGGGTCCCAGTATCTTCAGGGGTCTCCCCCTCCTCCTTCTCCCCAGTGGACTTCGAGTGTCCGTTGACCTCTCTGGCAGAAGCCACAGAGGCCAGGGCTGGCAGTTTGGCTGAGGCCAAAGCCCCACCATGGTCGGGTCGGGGCTGCTTGGACTCACCCTGCCCAGGCCCCCCCTTGGCCCTGGGACCTCTGCGGTTGCTGCGTTTGGCGATCAGGTAGATGCGCAGGTAGACAAGGATCATGATGAGGCAAGGAGCAAAGAAAGATCCGATGCTGGAGGCCAGGATGTACCAGGCCTCCTGGTTGAGCTTGCACTGGGGGCGCCCGCGCGGCTGGGGGCCCTGGTCGCCCTTGTAGATGAGGGGCGGCAGCGAGATGACGGCGGCGATGAGCCACACAGTGAGGATGATGCACTTGATGCGGCGCGGGGTGCGCTTGGAGTTGTACTCCAGCGCGCGGCTCACGGCCCAGTAGCGGTCCAGGCTGATGGCGCACAGGTGCACGATGGACGAGGTGCAGAAGAGCACGTCGAGCGCCAGGTACACCTCGCACCACGTGCGCCGGAAGTACCAGTAGCCCAGCAGCTCGTTGGCCAGCGAGAAAGGGATGATGAGCGTGGCCACCAGGATGTCGGCGGCGGCCAGCGACACCAGGAACAGGTTCTGAGGGGCGCGCAGCGAGCGGCTGGTCAACACAGCCAGGATGACCAGAGCGTTGCCGAAGATGGTAAAGAGAATGAGGAAGGTGATGGCCGCCGCTATGGCCGCTGTGGCCTGCACGGAGTAGGGGTCCTGGTGGTCCATGACGGGGCGGGAGGTGGGCAGAGGGAGCGCTGCCCGCCCAGTGCGCACCGTGGACGACAGCGCTGCCCGGCTCGGCTAGACAAGAGCGTCGCCCCT", 96778623 - 1);
var codingRegion = new CodingRegion(96780545, 96781888, 97, 1449, 1344);
var regions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 1, 96778623, 96780986, 1008, 3371),
new TranscriptRegion(TranscriptRegionType.Exon, 1, 96780987, 96781984, 1, 998)
};
var rnaEdits = new IRnaEdit[]
{
new RnaEdit(999, 998, "AGAGGAGGA")
};
const byte startExonPhase = 0;
const bool onReverseStrand = true;
var codingSequence = new CdnaSequence(genomicSeq, codingRegion, regions, onReverseStrand, rnaEdits);
var expectedCodingSeq = "ATGGACCACCAGGACCCCTACTCCGTGCAGGCCACAGCGGCCATAGCGGCGGCCATCACCTTCCTCATTCTCTTTACCATCTTCGGCAACGCTCTGGTCATCCTGGCTGTGTTGACCAGCCGCTCGCTGCGCGCCCCTCAGAACCTGTTCCTGGTGTCGCTGGCCGCCGCCGACATCCTGGTGGCCACGCTCATCATCCCTTTCTCGCTGGCCAACGAGCTGCTGGGCTACTGGTACTTCCGGCGCACGTGGTGCGAGGTGTACCTGGCGCTCGACGTGCTCTTCTGCACCTCGTCCATCGTGCACCTGTGCGCCATCAGCCTGGACCGCTACTGGGCCGTGAGCCGCGCGCTGGAGTACAACTCCAAGCGCACCCCGCGCCGCATCAAGTGCATCATCCTCACTGTGTGGCTCATCGCCGCCGTCATCTCGCTGCCGCCCCTCATCTACAAGGGCGACCAGGGCCCCCAGCCGCGCGGGCGCCCCCAGTGCAAGCTCAACCAGGAGGCCTGGTACATCCTGGCCTCCAGCATCGGATCTTTCTTTGCTCCTTGCCTCATCATGATCCTTGTCTACCTGCGCATCTACCTGATCGCCAAACGCAGCAACCGCAGAGGTCCCAGGGCCAAGGGGGGGCCTGGGCAGGGTGAGTCCAAGCAGCCCCGACCCGACCATGGTGGGGCTTTGGCCTCAGCCAAACTGCCAGCCCTGGCCTCTGTGGCTTCTGCCAGAGAGGTCAACGGACACTCGAAGTCCACTGGGGAGAAGGAGGAGGGGGAGACCCCTGAAGATACTGGGACCCGGGCCTTGCCACCCAGTTGGGCTGCCCTTCCCAACTCAGGCCAGGGCCAGAAGGAGGGTGTTTGTGGGGCATCTCCAGAGGATGAAGCTGAAGAGGAGGAAGAGGAGGAGGAGGAGGAGGAAGAGTGTGAACCCCAGGCAGTGCCAGTGTCTCCGGCCTCAGCTTGCAGCCCCCCGCTGCAGCAGCCACAGGGCTCCCGGGTGCTGGCCACCCTACGTGGCCAGGTGCTCCTGGGCAGGGGCGTGGGTGCTATAGGTGGGCAGTGGTGGCGTCGACGGGCGCAGCTGACCCGGGAGAAGCGCTTCACCTTCGTGCTGGCTGTGGTCATTGGCGTTTTTGTGCTCTGCTGGTTCCCCTTCTTCTTCAGCTACAGCCTGGGAGCCATCTGCCCGAAGCACTGCAAGGTGCCCCATGGCCTCTTCCAGTTCTTCTTCTGGATCGGCTACTGCAACAGCTCACTGAACCCTGTTATCTACACCATCTTCAACCAGGACTTCCGCCGTGCCTTCCGGAGGATCCTGTGCCGCCCGTGGACCCAGACGGCCTGGTGA";
var rnaEditLength = rnaEdits[0].Bases.Length;
Assert.Equal(expectedCodingSeq, codingSequence.GetCdnaSequence().Substring(codingRegion.CdnaStart - 1, codingRegion.Length + rnaEditLength));
}
private static ITranscript GetGapTranscript()
{
//NM_000314.4
var regions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 1, 89623195, 89623860, 1, 666),
new TranscriptRegion(TranscriptRegionType.Gap, 1, 89623861, 89623861, 666, 667),
new TranscriptRegion(TranscriptRegionType.Exon, 1, 89623862, 89624305, 667, 1110),
new TranscriptRegion(TranscriptRegionType.Intron, 1, 89624306, 89653781, 1110, 1111),
new TranscriptRegion(TranscriptRegionType.Exon, 2, 89653782, 89653866, 1111, 1195),
new TranscriptRegion(TranscriptRegionType.Intron, 2, 89653867, 89685269, 1195, 1196),
new TranscriptRegion(TranscriptRegionType.Exon, 3, 89685270, 89685314, 1196, 1240),
new TranscriptRegion(TranscriptRegionType.Intron, 3, 89685315, 89690802, 1240, 1241),
new TranscriptRegion(TranscriptRegionType.Exon, 4, 89690803, 89690846, 1241, 1284),
new TranscriptRegion(TranscriptRegionType.Intron, 4, 89690847, 89692769, 1284, 1285),
new TranscriptRegion(TranscriptRegionType.Exon, 5, 89692770, 89693008, 1285, 1523),
new TranscriptRegion(TranscriptRegionType.Intron, 5, 89693009, 89711874, 1523, 1524),
new TranscriptRegion(TranscriptRegionType.Exon, 6, 89711875, 89712016, 1524, 1665),
new TranscriptRegion(TranscriptRegionType.Intron, 6, 89712017, 89717609, 1665, 1666),
new TranscriptRegion(TranscriptRegionType.Exon, 7, 89717610, 89717776, 1666, 1832),
new TranscriptRegion(TranscriptRegionType.Intron, 7, 89717777, 89720650, 1832, 1833),
new TranscriptRegion(TranscriptRegionType.Exon, 8, 89720651, 89720875, 1833, 2057),
new TranscriptRegion(TranscriptRegionType.Intron, 8, 89720876, 89725043, 2057, 2058),
new TranscriptRegion(TranscriptRegionType.Exon, 9, 89725044, 89728532, 2058, 5546)
};
var translation = new Mock <ITranslation>();
translation.SetupGet(x => x.CodingRegion).Returns(new CodingRegion(89624227, 89725229, 1032, 2243, 1212));
var rnaEdits = new IRnaEdit[3];
rnaEdits[0] = new RnaEdit(667, 667, null);
rnaEdits[1] = new RnaEdit(707, 707, "C");
rnaEdits[2] = new RnaEdit(5548, 5547, "AAAAAAAAAAAAAAAAAAAAAAAAAA");
var transcript = new Mock <ITranscript>();
transcript.SetupGet(x => x.Id).Returns(CompactId.Convert("NM_000314", 4));
transcript.SetupGet(x => x.Chromosome).Returns(ChromosomeUtilities.Chr10);
transcript.SetupGet(x => x.Start).Returns(89623195);
transcript.SetupGet(x => x.End).Returns(89728532);
transcript.SetupGet(x => x.Gene.OnReverseStrand).Returns(false);
transcript.SetupGet(x => x.TranscriptRegions).Returns(regions);
transcript.SetupGet(x => x.Translation).Returns(translation.Object);
transcript.SetupGet(x => x.TotalExonLength).Returns(5546);
transcript.SetupGet(x => x.RnaEdits).Returns(rnaEdits);
return(transcript.Object);
}
public void RnaEdits_snv_forward_no_utr()
{
//NR_002754.2
var genomicSeq = new SimpleSequence("actctggtttctcttcaaatcgtataaatctttcgccttttactaaagatttccgtggagagaaacgagtgtgagtctgaaaccaattttttgaggccttgcgtttattagcagggctt", 11968210);
var codingRegion = new CodingRegion(11968211, 11968329, 1, 119, 119);
var regions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 1, 11968211, 11968329, 1, 119)
};
var rnaEdits = new IRnaEdit[] { new RnaEdit(107, 107, "t") };
const byte startExonPhase = 0;
var codingSequence = new CdnaSequence(genomicSeq, codingRegion, regions, false, rnaEdits);
Assert.Equal("actctggtttctcttcaaatcgtataaatctttcgccttttactaaagatttccgtggagagaaacgagtgtgagtctgaaaccaattttttgaggccttgcgttttttagcagggctt", codingSequence.GetCdnaSequence());
}
public static VariantType GetRnaEditType(IRnaEdit rnaEdit)
{
if (string.IsNullOrEmpty(rnaEdit.Bases))
{
return(VariantType.deletion);
}
if (rnaEdit.Start == rnaEdit.End && rnaEdit.Bases.Length == 1)
{
return(VariantType.SNV);
}
if (rnaEdit.Start == rnaEdit.End + 1 && !string.IsNullOrEmpty(rnaEdit.Bases))
{
return(VariantType.insertion);
}
if (Math.Abs(rnaEdit.End - rnaEdit.Start) + 1 == rnaEdit.Bases.Length)
{
return(VariantType.MNV);
}
return(VariantType.unknown);
}
private IRnaEdit[] ReadRnaEdits()
{
var cols = GetColumns("RnaEdits");
int numRnaEdits = int.Parse(cols[1]);
if (numRnaEdits == 0)
{
return(null);
}
var rnaEdits = new IRnaEdit[numRnaEdits];
var colIndex = 2;
for (var i = 0; i < numRnaEdits; i++)
{
int start = int.Parse(cols[colIndex++]);
int end = int.Parse(cols[colIndex++]);
string bases = cols[colIndex++];
rnaEdits[i] = new RnaEdit(start, end, bases);
}
return(rnaEdits);
}
public void RnaEdits_snv_forward_with_utr()
{
//NM_001144032.2 chr1:148644011-148644795
var genomicSeq = new SimpleSequence("ACTATAAAGACAGTGAAAAGATCAGTGGTTATCTTTGCAGACGCCACCATCGCTGTGAGCCCTGTACTATCAGCCATGGTCAACTCCGTCGTCTTTTTTGAAATCACCAGGGATGGCAAGCCCTTGGGCCGCATCTCCATCAAACTGTTTGCAGACAAGATTCCAAAGACAGCAGAAAACTTTCGTGCTCTGAGCACTGGAGAGAAAGGATTTCGTTATAAGGGTTCCTGCTTTCACAGAATTATTCCAGGGTTTATGTGTCAGGGTGGTGACTTCACACGCCCTAATGGCACCGGTGACAAGTCCATCTATGGGGAGAAATTTGATGATGAGAACCTCATCCGAAAGCATACAGGTTCTGGCATCTTGTCCATGGCAAATGCTGGACCCAACACAAATGGTTCCCAGTTTTTCATCTGTGCTGCCAAGACTGAGTGGTTGGATGGCAAGCATGTGGCGTTTGGCAAGGTGAAAGAACGTGTGAATATTGTGGAAGCCACGGAGCACTTTGGGTACAGGAATAGCAAGACCAGCAAGAAGATCACCATTGCTGACTGTGGACAATTCTAATGAGTTTGACTTGTGTTTTATTTTCACCACCAGACCCATTCCTTCTGTAGCTCAGGAGAGCACCCCTCCACCACATTTGCTTGCAATATCCTAGAATCTTTGTGCTCTTGCTGCAGTTCCCTTTGGGTTCCATGTTTTCCTTGTTCCCTTCCATGCCTAGCTGGATGGCAGAGTTGAGTTAAGTTTATGATTATGAAATAAAAACTAAGTAACAA", 148644011 - 1);
var codingRegion = new CodingRegion(148644086, 148644580, 76, 570, 495);
var regions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 1, 148644011, 148644795, 1, 785)
};
var rnaEdits = new IRnaEdit[]
{
new RnaEdit(420, 420, "C"),
new RnaEdit(500, 500, "T"),
new RnaEdit(737, 737, "T")
};
const byte startExonPhase = 0;
var codingSequence = new CdnaSequence(genomicSeq, codingRegion, regions, false, rnaEdits);
Assert.Equal("ATGGTCAACTCCGTCGTCTTTTTTGAAATCACCAGGGATGGCAAGCCCTTGGGCCGCATCTCCATCAAACTGTTTGCAGACAAGATTCCAAAGACAGCAGAAAACTTTCGTGCTCTGAGCACTGGAGAGAAAGGATTTCGTTATAAGGGTTCCTGCTTTCACAGAATTATTCCAGGGTTTATGTGTCAGGGTGGTGACTTCACACGCCCTAATGGCACCGGTGACAAGTCCATCTATGGGGAGAAATTTGATGATGAGAACCTCATCCGAAAGCATACAGGTTCTGGCATCTTGTCCATGGCAAATGCTGGACCCAACACAAATGGTTCCCAGTTTTTCATCTGCGCTGCCAAGACTGAGTGGTTGGATGGCAAGCATGTGGCGTTTGGCAAGGTGAAAGAACGTGTGAATATTGTGGAAGCCATGGAGCACTTTGGGTACAGGAATAGCAAGACCAGCAAGAAGATCACCATTGCTGACTGTGGACAATTCTAA", codingSequence.GetCdnaSequence().Substring(codingRegion.CdnaStart - 1, codingRegion.Length));
}
public int CompareTo(IRnaEdit other)
{
return(Start.CompareTo(other.Start));
}
