public void TranslateHardReverseStrand()
{
Genome genome = new Genome(Path.Combine(TestContext.CurrentContext.TestDirectory, "Homo_sapiens.GRCh38.dna.chromosome.14.fa"));
GeneModel geneModel = new GeneModel(genome, Path.Combine(TestContext.CurrentContext.TestDirectory, "HardReverseStrand", "reverse.gff3"));
List <Protein> proteins = geneModel.Translate(true).ToList();
ISequence codingSequence = new FastAParser().Parse(Path.Combine(TestContext.CurrentContext.TestDirectory, "HardReverseStrand", "codingSeq.fa")).First();
Assert.AreEqual(SequenceExtensions.ConvertToString(codingSequence),
SequenceExtensions.ConvertToString(geneModel.Genes[0].Transcripts[0].RetrieveCodingSequence()));
Assert.AreEqual("MNLQAQPKAQNKRKRCLFGGQEPAPKEQPPPLQPPQQSIRVKEEQYLGHEGPGGAVSTSQ" +
"PVELPPPSSLALLNSVVYGPERTSAAMLSQQVASVKWPNSVMAPGRGPERGGGGGVSDSS" +
"WQQQPGQPPPHSTWNCHSLSLYSATKGSPHPGVGVPTYYNHPEALKREKAGGPQLDRYVR" +
"PMMPQKVQLEVGRPQAPLNSFHAAKKPPNQSLPLQPFQLAFGHQVNRQVFRQGPPPPNPV" +
"AAFPPQKQQQQQQPQQQQQQQQAALPQMPLFENFYSMPQQPSQQPQDFGLQPAGPLGQSH" +
"LAHHSMAPYPFPPNPDMNPELRKALLQDSAPQPALPQVQIPFPRRSRRLSKEGILPPSAL" +
"DGAGTQPGQEATGNLFLHHWPLQQPPPGSLGQPHPEALGFPLELRESQLLPDGERLAPNG" +
"REREAPAMGSEEGMRAVSTGDCGQVLRGGVIQSTRRRRRASQEANLLTLAQKAVELASLQ" +
"NAKDGSGSEEKRKSVLASTTKCGVEFSEPSLATKRAREDSGMVPLIIPVSVPVRTVDPTE" +
"AAQAGGLDEDGKGPEQNPAEHKPSVIVTRRRSTRIPGTDAQAQAEDMNVKLEGEPSVRKP" +
"KQRPRPEPLIIPTKAGTFIAPPVYSNITPYQSHLRSPVRLADHPSERSFELPPYTPPPIL" +
"SPVREGSGLYFNAIISTSTIPAPPPITPKSAHRTLLRTNSAEVTPPVLSVMGEATPVSIE" +
"PRINVGSRFQAEIPLMRDRALAAADPHKADLVWQPWEDLESSREKQRQVEDLLTAACSSI" +
"FPGAGTNQELALHCLHESRGDILETLNKLLLKKPLRPHNHPLATYHYTGSDQWKMAERKL" +
"FNKGIAIYKKDFFLVQKLIQTKTVAQCVEFYYTYKKQVKIGRNGTLTFGDVDTSDEKSAQ" +
"EEVEVDIKTSQKFPRVPLPRRESPSEERLEPKREVKEPRKEGEEEVPEIQEKEEQEEGRE" +
"RSRRAAAVKATQTLQANESASDILILRSHESNAPGSAGGQASEKPREGTGKSRRALPFSE" +
"KKKKTETFSKTQNQENTFPCKKCGR",
proteins[0].BaseSequence);
}
public void TranslateReverseStrand()
{
Genome genome = new Genome(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "chr1_sample.fa"));
GeneModel geneModel = new GeneModel(genome, Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "chr1_one_transcript_reverse.gtf"));
List <Protein> proteins_wo_variant = geneModel.Translate(true).ToList();
Assert.AreEqual("FFYFIIWSLTLLPRAGLELLTSSDPPASASQSVGITGVSHHAQ",
proteins_wo_variant[0].BaseSequence);
}
public void TranslateAnotherReverseStrand()
{
// See http://useast.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000233306;r=7:38362864-38363518;t=ENST00000426402
Genome genome = new Genome(Path.Combine(TestContext.CurrentContext.TestDirectory, "Homo_sapiens.GRCh38.dna.chromosome.7.fa"));
GeneModel geneModel = new GeneModel(genome, Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "chr7_one_transcript_reverse.gtf"));
List <Protein> proteins = geneModel.Translate(true).ToList();
Assert.AreEqual("MQWALAVLLAFLSPASQKSSNLEGRTKSVIRQTGSSAEITCDLAEGSNGYIHWYLHQEGKAPQRLQYYDSYNSKVVLESGVSPGKYYTYASTRNNLRLILRNLIENDFGVYYCATWDG",
proteins[0].BaseSequence);
}
public void TranslateSelenocysteineContaining()
{
Genome genome = new Genome(Path.Combine(TestContext.CurrentContext.TestDirectory, "Homo_sapiens.GRCh38.dna.chromosome.5.fa"));
GeneModel geneModel = new GeneModel(genome, Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "chr5_selenocysteineContaining.gff3"));
GeneModel.GetImportantProteinAccessions(Path.Combine(TestContext.CurrentContext.TestDirectory, "Homo_sapiens.GRCh38.pep.all.fa"),
out Dictionary <string, string> p, out HashSet <string> bad, out Dictionary <string, string> se);
List <Protein> proteins = geneModel.Translate(true, bad, se).ToList();
Assert.AreEqual("MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSNGSVTVVALLQASUYLCILQASKLEDLRVKLKKEGYSNISYIVVNHQGISSRLKYTHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDRCGRLVYHLGLPFSFLTFPYVEEAIKIAYCEKKCGNCSLTTLKDEDFCKRVSLATVDKTVETPSPHYHHEHHHNHGHQHLGSSELSENQQPGAPNAPTHPAPPGLHHHHKHKGQHRQGHPENRDMPASEDLQDLQKKLCRKRCINQLLCKLPTDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPPAAUQISQQLIPTEASASURUKNQAKKUEUPSN",
proteins[0].BaseSequence);
}
public void TranslateMTSeq()
{
Genome genome = new Genome(Path.Combine(TestContext.CurrentContext.TestDirectory, "Homo_sapiens.GRCh38.dna.chromosome.MT.fa"));
GeneModel geneModel = new GeneModel(genome, Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "chrM_one_transcript_reverse.gtf"));
List <Protein> proteins = geneModel.Translate(true).ToList();
Assert.AreEqual("MPMANLLLLIVPILIAMAFLMLTERKILGYMQLRKGPNVVGPYGLLQPFADAMKLFTKEPLKPATSTITLYITAPTLALTIALLLWTPLPMPNPLVNLNLGLLFILATSSLAVYSILWSGWASNSNYALIGALRAVAQTISYE" +
"VTLAIILLSTLLMSGSFNLSTLITTQEHLWLLLPSWPLAMMWFISTLAETNRTPFDLAEGESELVSGFNIEYAAGPFALFFMAEYTNIIMMNTLTTTIFLGTTYDALSPELYTTYFVTKTLLLTSLFLWIRTAYPRFRYDQLMHLLWKNFLPLTLALLMWYVSMPITISSIPPQT",
proteins[0].BaseSequence);
geneModel = new GeneModel(genome, Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "chrM_one_transcript_reverse2.gtf"));
proteins = geneModel.Translate(true).ToList();
Assert.AreEqual("MNPLAQPVIYSTIFAGTLITALSSHWFFTWVGLEMNMLAFIPVLTKKMNPRSTEAAIKYFLTQATASMILLMAILFNNMLSGQWTMTNTTNQYSSLMIMMAMAMKLGMAPFHFWVPEVTQGTPLTSGLLLLTWQKLAPISIMYQISPS" +
"LNVSLLLTLSILSIMAGSWGGLNQTQLRKILAYSSITHMGWMMAVLPYNPNMTILNLTIYIILTTTAFLLLNLNSSTTTLLLSRTWNKLTWLTPLIPSTLLSLGGLPPLTGFLPKWAIIEEFTKNNSLIIPTIMATITLLNLYFYLRLIYSTSITLLPMSNNVKM" +
"KWQFEHTKPTPFLPTLIALTTLLLPISPFMLMIL",
proteins[0].BaseSequence);
}
/// <summary>
/// Times and checks that all proteins in the pep.all.fasta protein fasta file are the same as are output by this library
/// </summary>
private static void SameProteins()
{
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
// download and decompress references
string genomeFasta = "Homo_sapiens.GRCh38.dna.primary_assembly.fa";
string geneModelFile = "Homo_sapiens.GRCh38.81.gff3";
string proteinFasta = "Homo_sapiens.GRCh38.pep.all.fa";
string[] gunzippedFiles = new[] { genomeFasta, geneModelFile, proteinFasta };
if (!gunzippedFiles.All(f => File.Exists(f) && new FileInfo(f).Length > 0))
{
using (WebClient Client = new WebClient())
{
Client.DownloadFile(@"ftp://ftp.ensembl.org/pub/release-81//fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz", "Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz");
Client.DownloadFile(@"ftp://ftp.ensembl.org/pub/release-81/gff3/homo_sapiens/Homo_sapiens.GRCh38.81.gff3.gz", "Homo_sapiens.GRCh38.81.gff3.gz");
Client.DownloadFile(@"ftp://ftp.ensembl.org/pub/release-81//fasta/homo_sapiens/pep/Homo_sapiens.GRCh38.pep.all.fa.gz", "Homo_sapiens.GRCh38.pep.all.fa.gz");
}
}
foreach (var gunzippedFile in gunzippedFiles)
{
if (!File.Exists(gunzippedFile) || new FileInfo(gunzippedFile).Length == 0)
{
using (FileStream stream = new FileStream(gunzippedFile + ".gz", FileMode.Open))
using (GZipStream gunzip = new GZipStream(stream, CompressionMode.Decompress))
using (var f = File.Create(gunzippedFile))
{
gunzip.CopyTo(f);
}
}
}
GeneModel.GetImportantProteinAccessions(proteinFasta, out Dictionary <string, string> proteinAccessionSequence, out HashSet <string> bad, out Dictionary <string, string> se);
Genome genome = new Genome(genomeFasta);
GeneModel geneModel = new GeneModel(genome, geneModelFile);
List <Protein> geneBasedProteins = geneModel.Translate(true, bad, se);
List <Protein> pepDotAll = ProteinDbLoader.LoadProteinFasta(proteinFasta, true, DecoyType.None, false,
ProteinDbLoader.EnsemblAccessionRegex, ProteinDbLoader.EnsemblFullNameRegex, ProteinDbLoader.EnsemblFullNameRegex, ProteinDbLoader.EnsemblGeneNameRegex, null, out List <string> errors);
Dictionary <string, string> accSeq = geneBasedProteins.ToDictionary(p => p.Accession, p => p.BaseSequence);
stopwatch.Stop();
bool allAreEqual = true;
foreach (Protein p in pepDotAll)
{
// now handled with the badAccessions // && !p.BaseSequence.Contains('*') && !seq.Contains('*') && !p.BaseSequence.Contains('X'))
if (accSeq.TryGetValue(p.Accession, out string seq))
{
if (p.BaseSequence != seq)
{
allAreEqual = false;
break;
}
}
}
stopwatch.Stop();
Console.WriteLine("Finished checking that all proteins are the same.");
Console.WriteLine("Time elapsed: " + stopwatch.Elapsed.Minutes.ToString() + " minutes and " + stopwatch.Elapsed.Seconds.ToString() + " seconds.");
Console.WriteLine("Result: all proteins are " + (allAreEqual ? "" : "not ") + "equal ");
Console.WriteLine("Press any key to continue...");
Console.ReadKey();
foreach (var file in Directory.GetFiles(Environment.CurrentDirectory, Path.GetFileNameWithoutExtension(genomeFasta) + "*"))
{
File.Delete(file);
}
foreach (var file in Directory.GetFiles(Environment.CurrentDirectory, Path.GetFileNameWithoutExtension(geneModelFile) + "*"))
{
File.Delete(file);
}
foreach (var file in Directory.GetFiles(Environment.CurrentDirectory, Path.GetFileNameWithoutExtension(proteinFasta) + "*"))
{
File.Delete(file);
}
}
