Package org.snpeff.interval
Class Gene
- All Implemented Interfaces:
Serializable
,Cloneable
,Comparable<Interval>
,Iterable<Transcript>
,TxtSerializable
Interval for a gene, as well as transcripts
- Author:
- pcingola
- See Also:
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Nested Class Summary
Nested Classes -
Field Summary
FieldsFields inherited from class org.snpeff.interval.Interval
chromosomeNameOri, end, id, parent, start, strandMinus
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addPerGene
(Marker marker) Add a gene dependent markerboolean
adjust()
Adjust start, end and strand valuesvoid
Build gene dependent interval treeGet canonical transcript Canonical transcripts are defined as the longest CDS of amongst the protein coding transcripts.In a circular genome, a gene can have negative coordinates or crosses over chromosome end.Perform a shallow clonedouble
Calculate CpG bias: number of CpG / expected[CpG]void
filterTags
(Set<String> tags, Set<String> tagsNo) Filter transcripts by tagsvoid
Filter transcripts by TSLgeneType()
boolean
Is any of the transcripts protein coding?protected boolean
Show an error if parent does not include child?int
keepTranscripts
(Set<String> trIds) Remove all transcripts in trIdsint
Keep only protein coding transcriptsmarkers()
A list of all markers in this transcriptvoid
removeNonCanonical
(String trId) Remove all non-canonical transcriptsboolean
Remove unverified or corrected transcriptsvoid
serializeParse
(MarkerSerializer markerSerializer) Parse a line from a serialized fileserializeSave
(MarkerSerializer markerSerializer) Create a string to serialize to a filevoid
setBioType
(BioType bioType) int
Size of a genetic region for a given genetoString()
toString
(boolean showTr) boolean
variantEffect
(Variant variant, VariantEffects variantEffects) Get some details about the effect on this geneprotected void
variantEffectGene
(Variant variant, VariantEffects variantEffects) Add gene-specific annotationsMethods inherited from class org.snpeff.interval.IntervalAndSubIntervals
add, addAll, addAll, apply, clone, containsId, get, invalidateSorted, iterator, numChilds, query, remove, reset, setStrandMinus, shiftCoordinates, sorted, sortedStrand, subIntervals
Methods inherited from class org.snpeff.interval.Marker
adjust, applyDel, applyDup, applyIns, applyMixed, codonTable, compareTo, compareToPos, distance, distanceBases, getParent, getType, idChain, idChain, idChain, includes, intersect, isAdjustIfParentDoesNotInclude, isDeferredAnalysis, minus, query, readTxt, shouldApply, union, variantEffectNonRef
Methods inherited from class org.snpeff.interval.Interval
equals, findParent, getChromosome, getChromosomeName, getChromosomeNameOri, getChromosomeNum, getEnd, getGenome, getGenomeName, getId, getStart, getStrand, hashCode, intersects, intersects, intersects, intersects, intersectSize, isCircular, isSameChromo, isStrandMinus, isStrandPlus, isValid, setChromosomeNameOri, setEnd, setId, setParent, setStart, size, toStr, toStringAsciiArt, toStrPos
Methods inherited from class java.lang.Object
equals, finalize, getClass, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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CIRCULAR_GENE_ID
- See Also:
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Constructor Details
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Gene
public Gene() -
Gene
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Method Details
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addPerGene
Add a gene dependent marker -
adjust
public boolean adjust()Adjust start, end and strand values- Returns:
- true if any adjustment was done
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buildPerGene
public void buildPerGene()Build gene dependent interval tree -
canonical
Get canonical transcript Canonical transcripts are defined as the longest CDS of amongst the protein coding transcripts. If none of the transcripts is protein coding, then it is the longest cDNA. -
circularClone
In a circular genome, a gene can have negative coordinates or crosses over chromosome end. These genes are mirrored to the opposite end of the chromosome so that they can be referenced by both circular coordinates. -
cloneShallow
Description copied from class:Marker
Perform a shallow clone- Overrides:
cloneShallow
in classIntervalAndSubIntervals<Transcript>
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cpgExonBias
public double cpgExonBias()Calculate CpG bias: number of CpG / expected[CpG] -
filterTags
Filter transcripts by tags- Parameters:
tags
- : Ttranscripts to keeptagsNo
- : Transcripts to remove
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filterTranscriptSupportLevel
Filter transcripts by TSL -
geneType
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getBioType
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getGeneName
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isProteinCoding
public boolean isProteinCoding()Is any of the transcripts protein coding? -
isShowWarningIfParentDoesNotInclude
protected boolean isShowWarningIfParentDoesNotInclude()Description copied from class:Marker
Show an error if parent does not include child?- Overrides:
isShowWarningIfParentDoesNotInclude
in classMarker
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keepTranscripts
Remove all transcripts in trIds- Returns:
- : Number of transcripts removed
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keepTranscriptsProteinCoding
public int keepTranscriptsProteinCoding()Keep only protein coding transcripts- Returns:
- : Number of transcripts removed
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markers
Description copied from class:IntervalAndSubIntervals
A list of all markers in this transcript- Overrides:
markers
in classIntervalAndSubIntervals<Transcript>
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removeNonCanonical
Remove all non-canonical transcripts -
removeUnverified
public boolean removeUnverified()Remove unverified or corrected transcripts- Returns:
- : True if ALL transcripts have been removed
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serializeParse
Parse a line from a serialized file- Specified by:
serializeParse
in interfaceTxtSerializable
- Overrides:
serializeParse
in classIntervalAndSubIntervals<Transcript>
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serializeSave
Create a string to serialize to a file- Specified by:
serializeSave
in interfaceTxtSerializable
- Overrides:
serializeSave
in classIntervalAndSubIntervals<Transcript>
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setBioType
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sizeof
Size of a genetic region for a given gene -
toString
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toString
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variantEffect
Get some details about the effect on this gene- Overrides:
variantEffect
in classMarker
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variantEffectGene
Add gene-specific annotations
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