Exemple #1
0
        /// <summary>
        /// Get the last coding exon
        /// </summary>
        /// <returns></returns>
        public Exon GetLastCodingExon()
        {
            List <CDS> cds = CdsSortedStrand;

            if (cds.Count == 0)
            {
                return(null);
            }
            if (LastCodingExon == null)
            {
                // Get transcription start position
                long cend = IsStrandPlus() ? cds.Last().OneBasedEnd : cds.Last().OneBasedStart;

                // Pick exon intersecting cdsStart (TSS)
                foreach (Exon exon in ExonsSortedStrand)
                {
                    if (exon.Intersects(cend))
                    {
                        LastCodingExon = exon;
                    }
                }

                // Sanity check
                if (LastCodingExon == null)
                {
                    throw new ArgumentException("Error: Cannot find first coding exon for transcript:\n" + this);
                }
            }
            return(LastCodingExon);
        }
Exemple #2
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        /// <summary>
        /// Analyze insertions in this transcript. Add changeEffect to 'changeEffect'
        /// </summary>
        /// <param name="exon"></param>
        /// <returns></returns>
        protected override bool ChangeCodon(Exon exon)
        {
            string netChange = Variant.NetChange(Transcript.IsStrandMinus());

            CodonsReference = CodonsRef();
            CodonsAlternate = CodonsAlt();

            EffectType effType;

            if (netChange.Length % CODON_SIZE != 0)
            {
                /**
                 * Length not multiple of CODON_SIZE => FRAME_SHIFT
                 *  E.g. :
                 *      Original:			AAA CCC GGG AAA CCC GGG AAA CCC GGG
                 *      Insert 'TT' pos 0:	TTA AAC CCG GGA AAC CCG GGA AAC CCG GG
                 *      Insert 'TT' pos 1:	ATT AAC CCG GGA AAC CCG GGA AAC CCG GG
                 *      Insert 'TT' pos 2:	AAT TAC CCG GGA AAC CCG GGA AAC CCG GG
                 */
                effType = EffectType.FRAME_SHIFT;
            }
            else if (CodonStartIndex == 0)
            {
                /**
                 * Length multiple of CODON_SIZE and insertion happens at codon boundary => CODON_INSERTION
                 *  E.g. :
                 *      Original:			AAA CCC GGG AAA CCC GGG AAA CCC GGG
                 *      Insert 'TTT' pos 0:	TTT AAA CCC GGG AAA CCC GGG AAA CCC GGG
                 */
                effType = EffectType.CODON_INSERTION;
            }
            else
            {
                /**
                 * Length multiple of CODON_SIZE and insertion does not happen at codon boundary => CODON_CHANGE_PLUS_CODON_INSERTION
                 *  E.g. :
                 *      Original:			AAA CCC GGG AAA CCC GGG AAA CCC GGG
                 *      Insert 'TTT' pos 1:	ATT TAA CCC GGG AAA CCC GGG AAA CCC GGG
                 *      Insert 'TTT' pos 2:	AAT TTA CCC GGG AAA CCC GGG AAA CCC GGG
                 */
                if (CodonsAlternate.ToUpper(CultureInfo.InvariantCulture).StartsWith(CodonsReference.ToUpper(CultureInfo.InvariantCulture)))
                {
                    /**
                     *  May be the inserted base are equal to the old ones.
                     *  E.g.
                     *      Original:			AAA CCC GGG AAA CCC GGG AAA CCC GGG
                     *      Insert 'AAA' pos 1:	AAA AAA CCC GGG AAA CCC GGG AAA CCC GGG
                     */
                    effType = EffectType.CODON_INSERTION;
                }
                else
                {
                    effType = EffectType.CODON_CHANGE_PLUS_CODON_INSERTION;
                }
            }

            Effect(exon, effType, false);

            return(true);
        }
        /// <summary>
        /// Get the simplest string describing the effect (this is mostly used for testcases)
        /// </summary>
        /// <param name="shortFormat"></param>
        /// <returns></returns>
        public string ToStringSimple(bool shortFormat)
        {
            string     transcriptId = "";
            Transcript tr           = GetTranscript();

            if (tr != null)
            {
                transcriptId = tr.ID;
            }

            string exonId = "";
            Exon   exon   = GetExon();
            //if (exon != null) exonId = exon.getId();

            string eff = Effect(shortFormat, true, true, false, false);

            if (eff != "")
            {
                return(eff);
            }
            if (exonId != "")
            {
                return(exonId);
            }
            if (transcriptId != "")
            {
                return(transcriptId);
            }

            return("NO EFFECT");
        }
Exemple #4
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        /// <summary>
        /// Create UTR regions for this transcript
        /// </summary>
        public List <UTR> CreateUTRs()
        {
            if (CodingDomainSequences.Count == 0)
            {
                return(UTRs);
            }

            List <Interval> missing = Exons.OfType <Interval>().ToList();

            foreach (Interval interval in UTRs.Concat(CodingDomainSequences.OfType <Interval>().ToList()))
            {
                missing = missing.SelectMany(i => i.Minus(interval)).ToList();
            }

            long codingMin = CodingDomainSequences.Select(c => c.OneBasedStart).Min();
            long codingMax = CodingDomainSequences.Select(c => c.OneBasedEnd).Max();

            foreach (Interval interval in missing)
            {
                Exon x = FindExon(interval);
                if (x == null)
                {
                    throw new ArgumentException("Cannot find exon for UTR: " + interval.ToString());
                }

                UTR toAdd = null;
                if (IsStrandPlus())
                {
                    if (interval.OneBasedEnd <= codingMin)
                    {
                        toAdd = new UTR5Prime(x, x.ChromosomeID, x.Source, x.Strand, interval.OneBasedStart, interval.OneBasedEnd);
                    }
                    else if (interval.OneBasedStart >= codingMax)
                    {
                        toAdd = new UTR3Prime(x, x.ChromosomeID, x.Source, x.Strand, interval.OneBasedStart, interval.OneBasedEnd);
                    }
                }
                else
                {
                    if (interval.OneBasedStart >= codingMax)
                    {
                        toAdd = new UTR5Prime(x, x.ChromosomeID, x.Source, x.Strand, interval.OneBasedStart, interval.OneBasedEnd);
                    }
                    else if (interval.OneBasedEnd <= codingMin)
                    {
                        toAdd = new UTR3Prime(x, x.ChromosomeID, x.Source, x.Strand, interval.OneBasedStart, interval.OneBasedEnd);
                    }
                }

                // OK?
                if (toAdd != null)
                {
                    UTRs.Add(toAdd);
                }
            }
            return(UTRs);
        }
Exemple #5
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        /// <summary>
        /// Find base at genomic coordinate 'pos'
        /// </summary>
        /// <param name="pos"></param>
        /// <returns></returns>
        public ISequence BaseAt(int pos)
        {
            CalcCdsStartEnd();
            Exon ex = FindExon(pos);

            if (ex == null)
            {
                return(null);
            }
            return(ex.basesAt(pos - ex.OneBasedStart, 1));
        }
        /// <summary>
        /// Analyze SNPs in this transcript. Add changeEffect to 'changeEffect'
        /// </summary>
        /// <param name="exon"></param>
        /// <returns></returns>
        protected override bool ChangeCodon(Exon exon)
        {
            // Get old and new codons
            CodonsReference = CodonsRef();
            CodonsAlternate = CodonsAlt();

            // Use a generic low priority variant, this allows 'AdditionalEffects' to override it
            Effect(exon, EffectType.CODON_CHANGE, true);

            if (CodonsReference == "")
            {
                VariantEffects.AddErrorWarning(Variant, ErrorWarningType.ERROR_MISSING_CDS_SEQUENCE);
            }

            return(true);
        }
Exemple #7
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        public string getSequence()
        {
            // Create UTR sequence
            StringBuilder sb = new StringBuilder();

            foreach (UTR5Prime utr in get5primeUtrs())
            {
                Exon      ex     = (Exon)utr.Parent;
                ISequence utrSeq = ex.Sequence;
                if (utr.Length() < utrSeq.Count)
                {
                    utrSeq = utrSeq.GetSubSequence(0, utr.Length());
                }                                                                                     // UTR5' may stop before end of exon
                sb.Append(SequenceExtensions.ConvertToString(utrSeq));
            }
            return(sb.ToString());
        }
        /// <summary>
        /// Set marker. Add some warnings if the marker relates to incomplete transcripts
        /// </summary>
        /// <param name="marker"></param>
        public void SetMarker(Interval marker)
        {
            Marker = marker;

            Transcript transcript = GetTranscript();

            if (transcript != null)
            {
                // Transcript level errors or warnings
                AddErrorWarningInfo(transcript.sanityCheck(Variant));

                // Exon level errors or warnings
                Exon exon = GetExon();
                if (exon != null)
                {
                    AddErrorWarningInfo(exon.SanityCheck(Variant));
                }
            }
        }
Exemple #9
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        public List <Intron> CreateIntrons()
        {
            Exon previous = null;

            foreach (Exon x in Exons)
            {
                if (previous == null)
                {
                    previous = x;
                    continue;
                }
                Intron intron = new Intron(this, x.ChromosomeID, x.Source, x.Strand, previous.OneBasedEnd + 1, x.OneBasedStart - 1);
                if (intron.Length() > 0)
                {
                    Introns.Add(intron);
                }
            }
            return(Introns);
        }
Exemple #10
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        private static MetadataListItem <List <string> > CDSFeatureMetadata(CDS cds, Exon exon)
        {
            string cdsAttributes = exon.GetGtfAttributes() + " protein_id \"" + (cds.Parent as Transcript).ProteinID + "\";";
            var    feature       = new MetadataListItem <List <string> >(cds.FeatureType, cdsAttributes);

            feature.SubItems["source"] = new List <string> {
                cds.Source.ToString()
            };
            feature.SubItems["start"] = new List <string> {
                cds.OneBasedStart.ToString()
            };
            feature.SubItems["end"] = new List <string> {
                cds.OneBasedEnd.ToString()
            };
            if (cds.Strand != ".")
            {
                feature.SubItems["strand"] = new List <string> {
                    cds.Strand.ToString()
                };
            }                                                                                                   // might take in features without strand later on
            return(feature);
        }
Exemple #11
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        /// <summary>
        /// Corrrects coordinates of end of coding sequence based on coding sequence length
        /// </summary>
        /// <param name="codingSequenceLength"></param>
        /// <returns></returns>
        public UTR3Prime EndFrameCorrection(long codingSequenceLength)
        {
            long endFrame = codingSequenceLength % 3;

            if (endFrame <= 0)
            {
                return(null);
            }                                   // nothing to do

            // First exon is not zero? => Create a UTR5 prime to compensate
            Exon      parent = (FindParent(typeof(Transcript)) as Transcript).GetLastCodingExon();
            UTR3Prime utr3   = null;

            if (IsStrandPlus())
            {
                long start = OneBasedEnd - (endFrame - 1);
                utr3 = new UTR3Prime(parent, parent.ChromosomeID, parent.Source, parent.Strand, start, OneBasedEnd);
            }
            else
            {
                long end = OneBasedStart + (endFrame - 1);
                utr3 = new UTR3Prime(parent, parent.ChromosomeID, parent.Source, parent.Strand, OneBasedStart, end);
            }

            // correct start or end coordinates
            if (IsStrandPlus())
            {
                OneBasedEnd -= endFrame;
            }
            else
            {
                OneBasedStart += endFrame;
            }

            return(utr3);
        }
Exemple #12
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        public List <MetadataListItem <List <string> > > GetFeatures()
        {
            var features     = new List <MetadataListItem <List <string> > >();
            var geneMetadata = GetGtfFeatureMetadata();

            features.Add(geneMetadata);
            List <Interval> exonsAndCds = Exons.OfType <Interval>().Concat(CodingDomainSequences).OrderBy(t => t.OneBasedStart).ToList(); // exons before cds; exons should come up first after stable sorting
            Exon            currentExon = null;

            foreach (Interval xc in exonsAndCds)
            {
                Exon x = xc as Exon;
                if (x != null)
                {
                    currentExon = x;
                    features.Add(x.GetGtfFeatureMetadata());
                }
                else
                {
                    features.Add(CDSFeatureMetadata(xc as CDS, currentExon));
                }
            }
            return(features);
        }
Exemple #13
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        /// <summary>
        /// Corrrects coordinates of end of coding sequence based on coding sequence length
        /// </summary>
        /// <param name="codingSequenceLength"></param>
        /// <returns></returns>
        public UTR5Prime StartFrameCorrection()
        {
            if (StartFrame <= 0)
            {
                return(null);
            }                                     // nothing to do

            // First exon is not zero? => Create a UTR5 prime to compensate
            Exon      parent = (FindParent(typeof(Transcript)) as Transcript).GetLastCodingExon();
            UTR5Prime utr5   = null;

            if (IsStrandPlus())
            {
                long end = OneBasedStart + (StartFrame - 1);
                utr5 = new UTR5Prime(parent, parent.Source, parent.ChromosomeID, parent.Strand, OneBasedStart, end, null);
            }
            else
            {
                long start = OneBasedEnd - (StartFrame - 1);
                utr5 = new UTR5Prime(parent, parent.Source, parent.ChromosomeID, parent.Strand, start, OneBasedEnd, null);
            }

            // correct start or end coordinates
            if (IsStrandPlus())
            {
                OneBasedStart += StartFrame;
            }
            else
            {
                OneBasedEnd -= StartFrame;
            }

            StartFrame = 0;

            return(utr5);
        }
Exemple #14
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 protected UTR(Exon parent, string chromID, string source, string strand, long oneBasedStart, long oneBasedEnd)
     : base(parent, chromID, source, strand, oneBasedStart, oneBasedEnd)
 {
 }
Exemple #15
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 protected UTR(Exon parent, string chromID, string source, string strand, long oneBasedStart, long oneBasedEnd, HashSet <Variant> variants)
     : base(parent, chromID, source, strand, oneBasedStart, oneBasedEnd, variants)
 {
 }
        /// <summary>
        /// Processes a feature from a GFF3 gene model file.
        /// </summary>
        /// <param name="feature"></param>
        /// <param name="oneBasedStart"></param>
        /// <param name="oneBasedEnd"></param>
        /// <param name="chrom"></param>
        /// <param name="attributes"></param>
        public void ProcessGff3Feature(MetadataListItem <List <string> > feature, long oneBasedStart, long oneBasedEnd, Chromosome chrom, Dictionary <string, string> attributes)
        {
            bool hasGeneId       = attributes.TryGetValue("gene_id", out string geneId);
            bool hasTranscriptId = attributes.TryGetValue("transcript_id", out string transcriptId);
            bool hasExonId       = attributes.TryGetValue("exon_id", out string exonId);
            bool hasProteinId    = attributes.TryGetValue("protein_id", out string proteinId);
            bool hasSource       = feature.SubItems.TryGetValue("source", out List <string> sourceish); // false if empty ("." in GFF format)
            bool hasStrand       = feature.SubItems.TryGetValue("strand", out List <string> strandish); // false if empty ("." in GFF format)
            bool hasFrame        = feature.SubItems.TryGetValue("frame", out List <string> framey);     // false if empty ("." in GFF format)

            string source = hasSource ? sourceish[0] : "";

            if (!hasStrand)
            {
                return;
            }                           // strand is a required to do anything in this program
            string strand = strandish[0];
            int    frame  = 0;

            if (hasFrame)
            {
                int.TryParse(framey[0], out frame);
            }

            if (hasGeneId && (currentGene == null || hasGeneId && geneId != currentGene.ID))
            {
                currentGene = new Gene(geneId, chrom, source, strand, oneBasedStart, oneBasedEnd, feature);
                Genes.Add(currentGene);
                GenomeForest.Add(currentGene);
            }

            if (hasTranscriptId && (currentTranscript == null || hasTranscriptId && transcriptId != currentTranscript.ID))
            {
                if (currentTranscript != null)
                {
                    Transcript.SetRegions(currentTranscript);
                    currentTranscript.FrameCorrection();
                }
                currentTranscript = new Transcript(transcriptId, currentGene, source, strand, oneBasedStart, oneBasedEnd, null, null, feature);
                currentGene.Transcripts.Add(currentTranscript);
                GenomeForest.Add(currentTranscript);
            }

            if (hasExonId)
            {
                ISequence exon_dna = chrom.Sequence.GetSubSequence(oneBasedStart - 1, oneBasedEnd - oneBasedStart + 1);
                Exon      exon     = new Exon(currentTranscript, currentTranscript.IsStrandPlus() ? exon_dna : exon_dna.GetReverseComplementedSequence(),
                                              source, oneBasedStart, oneBasedEnd, chrom == null ? "" : chrom.ChromosomeID, strand, null, feature);
                if (exon.Length() > 0)
                {
                    currentTranscript.Exons.Add(exon);
                }
            }
            else if (hasProteinId)
            {
                CDS cds = new CDS(currentTranscript, chrom.Sequence.ID, source, strand, oneBasedStart, oneBasedEnd, null, frame);
                if (cds.Length() > 0)
                {
                    currentTranscript.CodingDomainSequences.Add(cds);
                    currentTranscript.ProteinID = proteinId;
                }
            }
            else // nothing to do
            {
            }
        }
        /// <summary>
        /// Processes a feature from a GTF gene model file.
        /// </summary>
        /// <param name="feature"></param>
        /// <param name="oneBasedStart"></param>
        /// <param name="oneBasedEnd"></param>
        /// <param name="chrom"></param>
        /// <param name="attributes"></param>
        public void ProcessGtfFeature(MetadataListItem <List <string> > feature, long oneBasedStart, long oneBasedEnd, Chromosome chrom, Dictionary <string, string> attributes)
        {
            bool hasGeneId       = attributes.TryGetValue("gene_id", out string geneId);
            bool hasTranscriptId = attributes.TryGetValue("transcript_id", out string transcriptId);
            bool hasProteinId    = attributes.TryGetValue("protein_id", out string proteinId);
            bool hasExonId       = attributes.TryGetValue("exon_id", out string exonId);
            bool hasSource       = feature.SubItems.TryGetValue("source", out List <string> sourceish);
            bool hasStrand       = feature.SubItems.TryGetValue("strand", out List <string> strandish);
            bool hasFrame        = feature.SubItems.TryGetValue("frame", out List <string> framey);

            string source = hasSource ? sourceish[0] : "";

            if (!hasStrand)
            {
                return;
            }                           // strand is a required to do anything in this program
            string strand = strandish[0];
            int    frame  = 0;

            if (hasFrame)
            {
                int.TryParse(framey[0], out frame);
            }

            // Trim prefixes from the IDs
            string genePrefix       = "gene:";
            string transcriptPrefix = "transcript:";

            if (hasGeneId && geneId.StartsWith(genePrefix))
            {
                string newGeneId = geneId.Substring(genePrefix.Length);
                feature.FreeText.Replace(geneId, newGeneId);
                geneId = newGeneId;
            }
            if (hasTranscriptId && transcriptId.StartsWith(transcriptPrefix))
            {
                string newTranscriptId = transcriptId.Substring(transcriptPrefix.Length);
                feature.FreeText.Replace(transcriptId, newTranscriptId);
                transcriptId = newTranscriptId;
            }
            if (hasProteinId && proteinId.StartsWith(transcriptPrefix))
            {
                proteinId = proteinId.Substring(transcriptPrefix.Length); // transcript id is used for protein id sometimes
            }

            // Catch the transcript features before they go by if available, i.e. if the file doesn't just have exons
            if (feature.Key == "transcript" && (currentTranscript == null || hasTranscriptId && transcriptId != currentTranscript.ID))
            {
                if (currentGene == null || hasGeneId && geneId != currentGene.ID)
                {
                    currentGene = new Gene(geneId, chrom, source, strand, oneBasedStart, oneBasedEnd, feature);
                    Genes.Add(currentGene);
                    GenomeForest.Add(currentGene);
                }

                currentTranscript = new Transcript(transcriptId, currentGene, source, strand, oneBasedStart, oneBasedEnd, null, null, feature);
                currentGene.Transcripts.Add(currentTranscript);
                GenomeForest.Add(currentTranscript);
            }

            if (feature.Key == "exon" || feature.Key == "CDS")
            {
                if (currentGene == null || hasGeneId && geneId != currentGene.ID)
                {
                    currentGene = new Gene(geneId, chrom, source, strand, oneBasedStart, oneBasedEnd, feature);
                    Genes.Add(currentGene);
                    GenomeForest.Add(currentGene);
                }

                if (currentTranscript == null || hasTranscriptId && transcriptId != currentTranscript.ID)
                {
                    if (currentTranscript != null)
                    {
                        Transcript.SetRegions(currentTranscript);
                        currentTranscript.FrameCorrection();
                    }
                    currentTranscript = new Transcript(transcriptId, currentGene, source, strand, oneBasedStart, oneBasedEnd, null, null, feature);
                    currentGene.Transcripts.Add(currentTranscript);
                    GenomeForest.Add(currentTranscript);
                }

                if (feature.Key == "exon")
                {
                    ISequence exon_dna = chrom.Sequence.GetSubSequence(oneBasedStart - 1, oneBasedEnd - oneBasedStart + 1);
                    Exon      exon     = new Exon(currentTranscript, currentTranscript.IsStrandPlus() ? exon_dna : exon_dna.GetReverseComplementedSequence(),
                                                  source, oneBasedStart, oneBasedEnd, chrom.Sequence.ID, strand, null, feature);
                    if (exon.Length() > 0)
                    {
                        currentTranscript.Exons.Add(exon);
                    }
                }
                else if (feature.Key == "CDS")
                {
                    CDS cds = new CDS(currentTranscript, chrom.Sequence.ID, source, strand, oneBasedStart, oneBasedEnd, null, frame);
                    if (hasProteinId)
                    {
                        currentTranscript.ProteinID = proteinId;
                    }
                    if (cds.Length() > 0)
                    {
                        currentTranscript.CodingDomainSequences.Add(cds);
                    }
                }
                else
                { // nothing to do
                }
            }
        }
Exemple #18
0
 /// <summary>
 /// Calculate the effect on an exon
 /// </summary>
 /// <param name="exon"></param>
 /// <returns></returns>
 protected virtual bool ChangeCodon(Exon exon)
 {
     throw new InvalidOperationException("Unimplemented method codonChangeSingle() for\n\t\tVariant type : " + Variant.GetType().Name + "\n\t\tClass        : " + GetType().Name + "\n\t\tVariant      : " + Variant);
 }
Exemple #19
0
 public UTR3Prime(Exon parent, string chromID, string source, string strand, long oneBasedStart, long oneBasedEnd)
     : base(parent, chromID, source, strand, oneBasedStart, oneBasedEnd)
 {
 }
        public string ToString(bool useSeqOntology, bool useHgvs)
        {
            // Get data to show
            string geneId = "", geneName = "", transcriptId = "", exonId = "", customId = "";
            string bioType  = null;
            int    exonRank = -1;

            if (Marker != null)
            {
                // Gene Id, name and biotype
                Gene       gene = GetGene();
                Transcript tr   = GetTranscript();

                // CDS size info
                if (gene != null)
                {
                    geneId = gene.ID;
                    //geneName = gene.getGeneName();
                    //bioType = (getBiotype() == null ? "" : getBiotype().ToString());
                }

                // Update trId
                if (tr != null)
                {
                    transcriptId = tr.ID;
                }

                // Exon rank information
                Exon exon = GetExon();
                //if (exon != null)
                //{
                //    exonId = exon.ID;
                //    exonRank = exon.getRank();
                //}

                // Regulation
                //if (isRegulation()) bioType = ((Regulation)marker).getRegulationType();
            }

            // Add seqChage's ID
            //if (!variant.getId() == "") customId += variant.getId();

            // Add custom markers
            //if (marker != null && marker is Custom) customId += (customId == "" ? "" : ";") + marker.getId();

            // CDS length
            long cdsSize = GetCdsLength();

            string error   = String.Join(",", Error);
            string warning = String.Join(",", Warning);
            string errWarn = error + (error == "" ? "" : "|") + warning;

            //string aaChange = "";

            //if (useHgvs) aaChange = getHgvs();
            //else aaChange = ((aaRef.Length + aaAlt.Length) > 0 ? aaRef + "/" + aaAlt : "");

            string aaChange = ((ReferenceAA.Length + AlternateAA.Length) > 0 ? ReferenceAA + "/" + AlternateAA : "");

            return(errWarn                                                                                 //
                   + "\t" + geneId                                                                         //
                   + "\t" + geneName                                                                       //
                   + "\t" + bioType                                                                        //
                   + "\t" + transcriptId                                                                   //
                   + "\t" + exonId                                                                         //
                   + "\t" + (exonRank >= 0 ? exonRank.ToString() : "")                                     //
                   + "\t" + Effect(false, false, false, useSeqOntology, false)                             //
                   + "\t" + aaChange                                                                       //
                   + "\t" + ((CodonsRef.Length + CodonsAlt.Length) > 0 ? CodonsRef + "/" + CodonsAlt : "") //
                   + "\t" + (CodonNum >= 0 ? (CodonNum + 1).ToString() : "")                               //
                                                                                                           //+ "\t" + (codonDegeneracy >= 0 ? codonDegeneracy + "" : "") //
                   + "\t" + (cdsSize >= 0 ? cdsSize.ToString() : "")                                       //
                   + "\t" + (CodonsAroundOld.Length > 0 ? CodonsAroundOld + " / " + CodonsAroundNew : "")  //
                   + "\t" + (AroundOldAAs.Length > 0 ? AroundOldAAs + " / " + AroundNewAAs : "")           //
                   + "\t" + customId                                                                       //
                   );
        }
Exemple #21
0
 /// <summary>
 /// Find a CDS that matches exactly the exon
 /// </summary>
 /// <param name="exon"></param>
 /// <returns></returns>
 public CDS FindCds(Exon exon)
 {
     return(CodingDomainSequences.FirstOrDefault(c => exon.Includes(c)));
 }
Exemple #22
0
        /// <summary>
        /// Analyze deletions in this transcript.
        /// </summary>
        /// <param name="exon"></param>
        /// <returns></returns>
        protected override bool ChangeCodon(Exon exon)
        {
            // Is there any net effect?
            if (NetCodingSequenceChange == "")
            {
                return(false);
            }

            EffectType effType;

            if (Variant.Includes(exon))
            {
                /**
                 * An exon has been entirely removed
                 */
                CodonsReference  = "";
                CodonsAlternate  = "";
                CodonStartNumber = -1;
                CodonStartIndex  = -1;
                effType          = EffectType.EXON_DELETED;
            }
            else if (NetCodingSequenceChange.Length % CODON_SIZE != 0)
            {
                /**
                 * Length not multiple of CODON_SIZE => FRAME_SHIFT
                 *  E.g. :
                 *      Original:			AAA CCC GGG AAA CCC GGG AAA CCC GGG
                 *      Delete 'AA' pos 0:	ACC CGG GAA ACC CGG GAA ACC CGG G
                 *      Delete 'AA' pos 1:	ACC CGG GAA ACC CGG GAA ACC CGG G
                 *      Delete 'AC' pos 2:	AAC CGG GAA ACC CGG GAA ACC CGG G
                 */
                CodonsReference = CodonsRef();
                CodonsAlternate = "";
                effType         = EffectType.FRAME_SHIFT;
            }
            else if (CodonStartIndex == 0)
            {
                /**
                 * Length multiple of CODON_SIZE and insertion happens at codon boundary => CODON_DELETION
                 *  E.g. :
                 *      Original:			AAA CCC GGG AAA CCC GGG AAA CCC GGG
                 *      Delete 'AAA' pos 0:	CCC GGG AAA CCC GGG AAA CCC GGG
                 */
                CodonsReference = CodonsRef();
                CodonsAlternate = "";
                effType         = EffectType.CODON_DELETION;
            }
            else
            {
                /**
                 * Length multiple of CODON_SIZE and insertion does not happen at codon boundary => CODON_CHANGE_PLUS_CODON_DELETION
                 *  E.g. :
                 *      Original:			AAA CCC GGG AAA CCC GGG AAA CCC GGG
                 *      Delete 'AAC' pos 1:	ACC GGG AAA CCC GGG AAA CCC GGG
                 *      Delete 'ACC' pos 2:	AAC GGG AAA CCC GGG AAA CCC GGG
                 */
                CodonsReference = CodonsRef();
                CodonsAlternate = CodonsAlt();

                if (CodonsAlternate == "" || CodonsReference.StartsWith(CodonsAlternate))
                {
                    /**
                     * Note: It might happen that the last codon of the exon was deleted.
                     *       In this case there is no 'CODON_CHANGE'
                     * E.g.
                     *      Original:				AAA CCC GGG AAA CCC GGG AAA CCC GGG
                     *      Delete 'GGG' pos 24:	ACC CCC GGG AAA CCC GGG AAA CCC
                     *
                     * Note2: It may also be the case that the deleted bases are equal to the following ones.
                     *  E.g.
                     *      Original:			ACG TCG TCC GGG AAA CCC GGG AAA CCC GGG
                     *      Delete 'CGT' pos 1:	ACG TCC GGG AAA CCC GGG AAA CCC GGG
                     */
                    effType = EffectType.CODON_DELETION;
                }
                else
                {
                    effType = EffectType.CODON_CHANGE_PLUS_CODON_DELETION;
                }
            }

            Effect(exon, effType, false);

            return(true);
        }
Exemple #23
0
 public UTR3Prime(Exon parent, string chromID, string source, string strand, long oneBasedStart, long oneBasedEnd, HashSet <Variant> variants)
     : base(parent, chromID, source, strand, oneBasedStart, oneBasedEnd, variants)
 {
 }
Exemple #24
0
 /// <summary>
 /// Copy an exon
 /// </summary>
 /// <param name="x"></param>
 public Exon(Exon x)
     : this(x.Parent as Transcript, x.Sequence, x.Source, x.OneBasedStart, x.OneBasedEnd, x.ChromosomeID, x.Strand, x.FeatureMetadata)
 {
 }