Package org.biojava.nbio.genome
Class GeneFeatureHelper
- java.lang.Object
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- org.biojava.nbio.genome.GeneFeatureHelper
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public class GeneFeatureHelper extends java.lang.Object
- Author:
- Scooter Willis
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Constructor Summary
Constructors Constructor Description GeneFeatureHelper()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
addGeneIDGFF2GeneFeatures(java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)
Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequencesstatic void
addGeneMarkGTFGeneFeatures(java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)
static void
addGlimmerGFF3GeneFeatures(java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)
static void
addGmodGFF3GeneFeatures(java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes)
Load GFF3 file using mRNA as the gene feature as not all GFF3 files are completestatic java.util.LinkedHashMap<java.lang.String,ChromosomeSequence>
getChromosomeSequenceFromDNASequence(java.util.LinkedHashMap<java.lang.String,DNASequence> dnaSequenceList)
static java.util.LinkedHashMap<java.lang.String,GeneSequence>
getGeneSequences(java.util.Collection<ChromosomeSequence> chromosomeSequences)
static java.util.LinkedHashMap<java.lang.String,ProteinSequence>
getProteinSequences(java.util.Collection<ChromosomeSequence> chromosomeSequences)
static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence>
loadFastaAddGeneFeaturesFromGeneIDGFF2(java.io.File fastaSequenceFile, java.io.File gffFile)
Loads Fasta file and GFF2 feature file generated from the geneid prediction algorithmstatic java.util.LinkedHashMap<java.lang.String,ChromosomeSequence>
loadFastaAddGeneFeaturesFromGeneMarkGTF(java.io.File fastaSequenceFile, java.io.File gffFile)
static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence>
loadFastaAddGeneFeaturesFromGlimmerGFF3(java.io.File fastaSequenceFile, java.io.File gffFile)
static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence>
loadFastaAddGeneFeaturesFromGmodGFF3(java.io.File fastaSequenceFile, java.io.File gffFile, boolean lazyloadsequences)
Lots of variations in the ontology or descriptors that can be used in GFF3 which requires writing a custom parser to handle a GFF3 generated or used by a specific application.static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence>
loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(java.io.File fastaSequenceFile, java.io.File uppercaseFastaFile, boolean throwExceptionGeneNotFound)
static void
main(java.lang.String[] args)
static void
outputFastaSequenceLengthGFF3(java.io.File fastaSequenceFile, java.io.File gffFile)
Output a gff3 feature file that will give the length of each scaffold/chromosome in the fasta file.
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Method Detail
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loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile
public static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(java.io.File fastaSequenceFile, java.io.File uppercaseFastaFile, boolean throwExceptionGeneNotFound) throws java.lang.Exception
- Throws:
java.lang.Exception
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outputFastaSequenceLengthGFF3
public static void outputFastaSequenceLengthGFF3(java.io.File fastaSequenceFile, java.io.File gffFile) throws java.lang.Exception
Output a gff3 feature file that will give the length of each scaffold/chromosome in the fasta file. Used for gbrowse so it knows length.- Parameters:
fastaSequenceFile
-gffFile
-- Throws:
java.lang.Exception
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loadFastaAddGeneFeaturesFromGeneIDGFF2
public static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGeneIDGFF2(java.io.File fastaSequenceFile, java.io.File gffFile) throws java.lang.Exception
Loads Fasta file and GFF2 feature file generated from the geneid prediction algorithm- Parameters:
fastaSequenceFile
-gffFile
-- Returns:
- Throws:
java.lang.Exception
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addGeneIDGFF2GeneFeatures
public static void addGeneIDGFF2GeneFeatures(java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws java.lang.Exception
Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequences- Parameters:
chromosomeSequenceList
-listGenes
-- Throws:
java.lang.Exception
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getChromosomeSequenceFromDNASequence
public static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> getChromosomeSequenceFromDNASequence(java.util.LinkedHashMap<java.lang.String,DNASequence> dnaSequenceList)
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loadFastaAddGeneFeaturesFromGmodGFF3
public static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGmodGFF3(java.io.File fastaSequenceFile, java.io.File gffFile, boolean lazyloadsequences) throws java.lang.Exception
Lots of variations in the ontology or descriptors that can be used in GFF3 which requires writing a custom parser to handle a GFF3 generated or used by a specific application. Probably could be abstracted out but for now easier to handle with custom code to deal with gff3 elements that are not included but can be extracted from other data elements.- Parameters:
fastaSequenceFile
-gffFile
-lazyloadsequences
- If set to true then the fasta file will be parsed for accession id but sequences will be read from disk when needed to save memory- Returns:
- Throws:
java.lang.Exception
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addGmodGFF3GeneFeatures
public static void addGmodGFF3GeneFeatures(java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws java.lang.Exception
Load GFF3 file using mRNA as the gene feature as not all GFF3 files are complete- Parameters:
chromosomeSequenceList
-listGenes
-- Throws:
java.lang.Exception
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loadFastaAddGeneFeaturesFromGlimmerGFF3
public static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGlimmerGFF3(java.io.File fastaSequenceFile, java.io.File gffFile) throws java.lang.Exception
- Throws:
java.lang.Exception
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addGlimmerGFF3GeneFeatures
public static void addGlimmerGFF3GeneFeatures(java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws java.lang.Exception
- Throws:
java.lang.Exception
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loadFastaAddGeneFeaturesFromGeneMarkGTF
public static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGeneMarkGTF(java.io.File fastaSequenceFile, java.io.File gffFile) throws java.lang.Exception
- Throws:
java.lang.Exception
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addGeneMarkGTFGeneFeatures
public static void addGeneMarkGTFGeneFeatures(java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws java.lang.Exception
- Throws:
java.lang.Exception
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getProteinSequences
public static java.util.LinkedHashMap<java.lang.String,ProteinSequence> getProteinSequences(java.util.Collection<ChromosomeSequence> chromosomeSequences) throws java.lang.Exception
- Throws:
java.lang.Exception
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getGeneSequences
public static java.util.LinkedHashMap<java.lang.String,GeneSequence> getGeneSequences(java.util.Collection<ChromosomeSequence> chromosomeSequences) throws java.lang.Exception
- Throws:
java.lang.Exception
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main
public static void main(java.lang.String[] args) throws java.lang.Exception
- Throws:
java.lang.Exception
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