public class GeneFeatureHelper
extends java.lang.Object
Constructor and Description |
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GeneFeatureHelper() |
Modifier and Type | Method and Description |
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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 sequences
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static 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 complete
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static 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 algorithm
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static 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.
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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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public static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(java.io.File fastaSequenceFile, java.io.File uppercaseFastaFile, boolean throwExceptionGeneNotFound) throws java.lang.Exception
java.lang.Exception
public static void outputFastaSequenceLengthGFF3(java.io.File fastaSequenceFile, java.io.File gffFile) throws java.lang.Exception
fastaSequenceFile
- gffFile
- java.lang.Exception
public static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGeneIDGFF2(java.io.File fastaSequenceFile, java.io.File gffFile) throws java.lang.Exception
fastaSequenceFile
- gffFile
- java.lang.Exception
public static void addGeneIDGFF2GeneFeatures(java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws java.lang.Exception
chromosomeSequenceList
- listGenes
- java.lang.Exception
public static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> getChromosomeSequenceFromDNASequence(java.util.LinkedHashMap<java.lang.String,DNASequence> dnaSequenceList)
public static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGmodGFF3(java.io.File fastaSequenceFile, java.io.File gffFile, boolean lazyloadsequences) throws java.lang.Exception
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 memoryjava.lang.Exception
public static void addGmodGFF3GeneFeatures(java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws java.lang.Exception
chromosomeSequenceList
- listGenes
- java.lang.Exception
public static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGlimmerGFF3(java.io.File fastaSequenceFile, java.io.File gffFile) throws java.lang.Exception
java.lang.Exception
public static void addGlimmerGFF3GeneFeatures(java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws java.lang.Exception
java.lang.Exception
public static java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGeneMarkGTF(java.io.File fastaSequenceFile, java.io.File gffFile) throws java.lang.Exception
java.lang.Exception
public static void addGeneMarkGTFGeneFeatures(java.util.LinkedHashMap<java.lang.String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws java.lang.Exception
java.lang.Exception
public static java.util.LinkedHashMap<java.lang.String,ProteinSequence> getProteinSequences(java.util.Collection<ChromosomeSequence> chromosomeSequences) throws java.lang.Exception
java.lang.Exception
public static java.util.LinkedHashMap<java.lang.String,GeneSequence> getGeneSequences(java.util.Collection<ChromosomeSequence> chromosomeSequences) throws java.lang.Exception
java.lang.Exception
public static void main(java.lang.String[] args) throws java.lang.Exception
java.lang.Exception