Class Transcript

    • Constructor Detail

      • Transcript

        public Transcript()
      • Transcript

        public Transcript​(Gene gene,
                          int start,
                          int end,
                          boolean strandMinus,
                          java.lang.String id)
    • Method Detail

      • aaNumber2Pos

        public int[] aaNumber2Pos()
        Calculate chromosome position as function of Amino Acid number
      • aaNumber2Pos

        public int aaNumber2Pos​(int aaNum)
        Find a genomic position of the first base in a Amino Acid 'aaNum'
      • add

        public void add​(Cds cdsInt)
        Add a CDS
      • add

        public void add​(Intron intron)
        Add an intron
      • add

        public void add​(SpliceSite spliceSite)
        Add a SpliceSite
      • add

        public void add​(Utr utr)
        Add a UTR
      • adjust

        public boolean adjust()
        Adjust transcript coordinates
      • apply

        public Transcript apply​(Variant variant)
        Create a new transcript after applying changes in variant Note: If this transcript is unaffected, no new transcript is created (same transcript is returned)
        Overrides:
        apply in class IntervalAndSubIntervals<Exon>
        Returns:
        The marker result after applying variant
      • baseAt

        public java.lang.String baseAt​(int pos)
        Find base at genomic coordinate 'pos'
      • baseNumber2MRnaPos

        public int baseNumber2MRnaPos​(int pos)
        Calculate distance from transcript start to a position mRNA is roughly the same than cDNA. Strictly speaking mRNA has a poly-A tail and 5'cap.
      • baseNumberCds

        public int baseNumberCds​(int pos,
                                 boolean usePrevBaseIntron)
        Calculate base number in a CDS where 'pos' maps
        Parameters:
        usePrevBaseIntron - : When 'pos' is intronic this method returns: - if( usePrevBaseIntron== false) => The first base in the exon after 'pos' (i.e. first coding base after intron) - if( usePrevBaseIntron== true) => The last base in the exon before 'pos' (i.e. last coding base before intron)
      • baseNumberCds2Codon

        public java.lang.String baseNumberCds2Codon​(int cdsBaseNumber)
        Return a codon that includes 'cdsBaseNumber'
      • baseNumberCds2Pos

        public int[] baseNumberCds2Pos()
        Calculate chromosome position as function of CDS number
      • cds

        public java.lang.String cds()
        Retrieve coding sequence
      • cdsMarker

        public Marker cdsMarker()
        Create a marker of the coding region in this transcript
      • codonNumber2Pos

        public int[] codonNumber2Pos​(int codonNum)
        Return an array of 3 genomic positions where amino acid number 'aaNum' maps
        Returns:
        aa2pos[0], aa2pos[1], aa2pos[2] are the coordinates (within the chromosome) of the three bases conforming codon 'aaNum'. Any aa2pos[i] = -1 means that it could a base in the codon could not be mapped.
      • collapseZeroGap

        public boolean collapseZeroGap()
        Collapses exons having gaps of zero (i.e. exons that followed by other exons). Does the same for CDSs and UTRs.
        Returns:
        true of any exon in the transcript was 'collapsed'
      • cpgExonBias

        public double cpgExonBias()
        Calculate CpG bias: number of CpG / expected[CpG]
      • cpgExons

        public int cpgExons()
        Count total CpG in this transcript's exons
      • createSpliceSites

        public void createSpliceSites​(int spliceSiteSize,
                                      int spliceRegionExonSize,
                                      int spliceRegionIntronMin,
                                      int spliceRegionIntronMax)
        Find all splice sites.
      • createUpDownStream

        public void createUpDownStream​(int upDownLength)
        Creates a list of UP/DOWN stream regions (for each transcript) Upstream (downstream) stream is defined as upDownLength before (after) transcript
      • deleteRedundant

        public boolean deleteRedundant()
        Deletes redundant exons (i.e. exons that are totally included in other exons). Does the same for CDSs. Does the same for UTRs.
      • findCds

        public Cds findCds​(Exon exon)
        Find a CDS that matches exactly the exon
      • findExon

        public Exon findExon​(int pos)
        Return the an exon that intersects 'pos'
      • findExon

        public Exon findExon​(Marker marker)
        Return an exon intersecting 'marker' (first exon found)
      • findIntron

        public Intron findIntron​(int pos)
        Return an intron overlapping position 'pos'
      • findUtr

        public Utr findUtr​(int pos)
        Return the UTR that hits position 'pos'
        Returns:
        An UTR intersecting 'pos' (null if not found)
      • findUtrs

        public java.util.List<Utr> findUtrs​(Marker marker)
        Return the UTR that intersects 'marker' (null if not found)
      • frameCorrection

        public boolean frameCorrection()
        Correct exons based on frame information. E.g. if the frame information (form a genomic database file, such as a GTF) does not match the calculated frame, we correct exon's boundaries to make them match. This is performed in two stages: i) First exon is corrected by adding a fake 5'UTR ii) Other exons are corrected by changing the start (or end) coordinates.
      • get3primeUtrs

        public java.util.List<Utr3prime> get3primeUtrs()
        Create a list of 3 prime UTRs
      • get3primeUtrsSorted

        public java.util.List<Utr3prime> get3primeUtrsSorted()
      • get5primeUtrs

        public java.util.List<Utr5prime> get5primeUtrs()
        Create a list of 5 prime UTRs
      • get5primeUtrsSorted

        public java.util.List<Utr5prime> get5primeUtrsSorted()
      • getBioType

        public BioType getBioType()
      • getCds

        public java.util.List<Cds> getCds()
        Get all CDSs
      • getCdsEnd

        public int getCdsEnd()
      • getCdsStart

        public int getCdsStart()
      • getDownstream

        public Downstream getDownstream()
      • getFirstCodingExon

        public Exon getFirstCodingExon()
        Get first coding exon
      • getTss

        public Marker getTss()
        Create a TSS marker
      • getUpstream

        public Upstream getUpstream()
      • getUtrs

        public java.util.List<Utr> getUtrs()
        Get all UTRs
      • getVersion

        public java.lang.String getVersion()
      • hasError

        public boolean hasError()
        Does this transcript have any errors?
      • hasErrorOrWarning

        public boolean hasErrorOrWarning()
        Does this transcript have any errors?
      • hasTranscriptSupportLevelInfo

        public boolean hasTranscriptSupportLevelInfo()
      • hasWarning

        public boolean hasWarning()
        Does this transcript have any errors?
      • introns

        public java.util.List<Intron> introns()
        Get all introns (lazy init)
      • isAaCheck

        public boolean isAaCheck()
      • isAdjustIfParentDoesNotInclude

        protected boolean isAdjustIfParentDoesNotInclude​(Marker parent)
        Description copied from class: Marker
        Adjust parent if it does not include child?
        Overrides:
        isAdjustIfParentDoesNotInclude in class Marker
      • isCanonical

        public boolean isCanonical()
      • isChecked

        public boolean isChecked()
        Has this transcript been checked against CDS/DNA/AA sequences?
      • isCorrected

        public boolean isCorrected()
      • isDnaCheck

        public boolean isDnaCheck()
      • isDownstream

        public boolean isDownstream​(int pos)
      • isErrorProteinLength

        public boolean isErrorProteinLength()
        Check if coding length is multiple of 3 in protein coding transcripts
        Returns:
        true on Error
      • isErrorStartCodon

        public boolean isErrorStartCodon()
        Is the first codon a START codon?
      • isErrorStopCodonsInCds

        public boolean isErrorStopCodonsInCds()
        Check if protein sequence has STOP codons in the middle of the coding sequence
        Returns:
        true on Error
      • isIntron

        public boolean isIntron​(int pos)
      • isProteinCoding

        public boolean isProteinCoding()
      • isRibosomalSlippage

        public boolean isRibosomalSlippage()
      • isUpstream

        public boolean isUpstream​(int pos)
      • isUtr

        public boolean isUtr​(int pos)
      • isUtr

        public boolean isUtr​(Marker marker)
      • isUtr3

        public boolean isUtr3​(int pos)
      • isUtr5

        public boolean isUtr5​(int pos)
      • isWarningStopCodon

        public boolean isWarningStopCodon()
        Is the last codon a STOP codon?
      • mRna

        public java.lang.String mRna()
        Retrieve coding sequence AND the UTRs (mRNA = 5'UTR + CDS + 3'UTR) I.e. Concatenate all exon sequences
      • protein

        public java.lang.String protein()
        Protein sequence (amino acid sequence produced by this transcripts)
      • queryExon

        public Exon queryExon​(Marker interval)
        Return the first exon that intersects 'interval' (null if not found)
      • rankExons

        public boolean rankExons()
        Assign ranks to exons
      • resetCache

        public void resetCache()
      • resetExons

        public void resetExons()
      • setAaCheck

        public void setAaCheck​(boolean aaCheck)
      • setBioType

        public void setBioType​(BioType bioType)
      • setCanonical

        public void setCanonical​(boolean canonical)
      • setDnaCheck

        public void setDnaCheck​(boolean dnaCheck)
      • setProteinCoding

        public void setProteinCoding​(boolean proteinCoding)
      • setRibosomalSlippage

        public void setRibosomalSlippage​(boolean ribosomalSlippage)
      • setTranscriptSupportLevel

        public void setTranscriptSupportLevel​(TranscriptSupportLevel transcriptSupportLevel)
      • setVersion

        public void setVersion​(java.lang.String version)
      • sortCds

        public void sortCds()
      • spliceSites

        public java.util.List<SpliceSite> spliceSites()
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class Marker
      • toString

        public java.lang.String toString​(boolean full)
      • toStringAsciiArt

        public java.lang.String toStringAsciiArt​(boolean full)
        Show a transcript as an ASCII Art
      • utrFromCds

        public boolean utrFromCds​(boolean verbose)
        Calculate UTR regions from CDSs