Class Transcript

Method Details

• aaNumber2Pos

  public int[] aaNumber2Pos()

  Calculate chromosome position as function of Amino Acid number Note that returns the chromosomal position of the first base for each Amino Acid

  If you need the chromosomal position of each base

• 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 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 String baseNumberCds2Codon(int cdsBaseNumber)

  Return a codon that includes 'cdsBaseNumber'

• baseNumberCds2Pos

  public int[] baseNumberCds2Pos()

  Calculate chromosome position as function of CDS number

• baseNumberCds2Pos

  public int baseNumberCds2Pos(int cdsBaseNum)

• cds

  public String cds()

  Retrieve coding sequence

• cdsMarker

  public Marker cdsMarker()

  Create a marker of the coding region in this transcript

• cloneShallow

  public Transcript cloneShallow()

  Description copied from class: Marker

  Perform a shallow clone

  Overrides:

  cloneShallow in class IntervalAndSubIntervals<Exon>

• 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.

  Bases in the array are sorted by chromosome position, so aa2pos[0] < aa2pos[1] < aa2pos[2]

• 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 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 List<Utr3prime> get3primeUtrs()

  Create a list of 3 prime UTRs

• get3primeUtrsSorted

  public List<Utr3prime> get3primeUtrsSorted()

• get5primeUtrs

  public List<Utr5prime> get5primeUtrs()

  Create a list of 5 prime UTRs

• get5primeUtrsSorted

  public List<Utr5prime> get5primeUtrsSorted()

• getBioType

  public BioType getBioType()

• getCds

  public List<Cds> getCds()

  Get all CDSs

• getCdsEnd

  public int getCdsEnd()

• getCdsStart

  public int getCdsStart()

• getDownstream

  public Downstream getDownstream()

• getExons

  public Collection<Exon> getExons()

  A more intuitive name for 'subintervals'

• getFirstCodingExon

  public Exon getFirstCodingExon()

  Get first coding exon

• getGene

  public Gene getGene()

• hasProteinId

  public boolean hasProteinId()

• getProteinId

  public String getProteinId()

• getTags

  public String[] getTags()

• getTranscriptSupportLevel

  public TranscriptSupportLevel getTranscriptSupportLevel()

• getTss

  public Marker getTss()

  Create a TSS marker

• getUpstream

  public Upstream getUpstream()

• getUtrs

  public List<Utr> getUtrs()

  Get all UTRs

• getVersion

  public String getVersion()

• setVersion

  public void setVersion(String version)

• hasCds

  public boolean hasCds()

• hasError

  public boolean hasError()

  Does this transcript have any errors?

• hasErrorOrWarning

  public boolean hasErrorOrWarning()

  Does this transcript have any errors?

• hasTag

  public boolean hasTag(String tag)

  Does this transcript have 'tag'?

• hasTags

  public boolean hasTags()

• hasTranscriptSupportLevelInfo

  public boolean hasTranscriptSupportLevelInfo()

• hasWarning

  public boolean hasWarning()

  Does this transcript have any errors?

• introns

  public List<Intron> introns()

  Get all introns (lazy init)

• isAaCheck

  public boolean isAaCheck()

• setAaCheck

  public void setAaCheck(boolean aaCheck)

• 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()

• setDnaCheck

  public void setDnaCheck(boolean dnaCheck)

• 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()

• setRibosomalSlippage

  public void setRibosomalSlippage(boolean ribosomalSlippage)

• 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?

• markers

  public Markers markers()

  A list of all markers in this transcript

  Overrides:

  markers in class IntervalAndSubIntervals<Exon>

• mRna

  public String mRna()

  Retrieve coding sequence AND the UTRs (mRNA = 5'UTR + CDS + 3'UTR) I.e. Concatenate all exon sequences

• protein

  public String protein()

  Protein sequence (amino acid sequence produced by this transcripts)

• query

  public Markers query(Marker marker)

  Query all genomic regions that intersect 'marker'

  Overrides:

  query in class IntervalAndSubIntervals<Exon>

• 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

• reset

  public void reset()

  Description copied from class: IntervalAndSubIntervals

  Remove all intervals

  Overrides:

  reset in class IntervalAndSubIntervals<Exon>

• resetCache

  public void resetCache()

• resetExons

  public void resetExons()

• sanityCheck

  public ErrorWarningType sanityCheck(Variant variant)

  Perfom some baseic chekcs, return error type, if any

• serializeParse

  public void serializeParse(MarkerSerializer markerSerializer)

  Parse a line from a serialized file

  Specified by:

  serializeParse in interface TxtSerializable

  Overrides:

  serializeParse in class IntervalAndSubIntervals<Exon>

• serializeSave

  public String serializeSave(MarkerSerializer markerSerializer)

  Create a string to serialize to a file

  Specified by:

  serializeSave in interface TxtSerializable

  Overrides:

  serializeSave in class IntervalAndSubIntervals<Exon>

• setBioType

  public void setBioType(BioType bioType)

• setCanonical

  public void setCanonical(boolean canonical)

• setProteinCoding

  public void setProteinCoding(boolean proteinCoding)

• setProteinId

  public void setProteinId(String proteinId)

• setTags

  public void setTags(String tags)

• setTranscriptSupportLevel

  public void setTranscriptSupportLevel(TranscriptSupportLevel transcriptSupportLevel)

• sortCds

  public void sortCds()

• spliceSites

  public List<SpliceSite> spliceSites()

• toString

  public String toString()

  Overrides:

  toString in class Marker

• toString

  public String toString(boolean full)

• toStringAsciiArt

  public String toStringAsciiArt(boolean full)

  Show a transcript as an ASCII Art

• utrFromCds

  public boolean utrFromCds(boolean verbose)

  Calculate UTR regions from CDSs

• variantEffect

  public boolean variantEffect(Variant variant, VariantEffects variantEffects)

  Get some details about the effect on this transcript

  Overrides:

  variantEffect in class Marker