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java.lang.Objectorg.biojava3.genome.GeneFeatureHelper
public class GeneFeatureHelper
Constructor Summary | |
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GeneFeatureHelper()
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Method Summary | |
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static void |
addGeneIDGFF2GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList,
FeatureList listGenes)
Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequences |
static void |
addGeneMarkGTFGeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList,
FeatureList listGenes)
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static void |
addGlimmerGFF3GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList,
FeatureList listGenes)
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static void |
addGmodGFF3GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList,
FeatureList listGenes)
Load GFF3 file using mRNA as the gene feature as not all GFF3 files are complete |
static LinkedHashMap<String,ChromosomeSequence> |
getChromosomeSequenceFromDNASequence(LinkedHashMap<String,DNASequence> dnaSequenceList)
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static LinkedHashMap<String,GeneSequence> |
getGeneSequences(Collection<ChromosomeSequence> chromosomeSequences)
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static LinkedHashMap<String,ProteinSequence> |
getProteinSequences(Collection<ChromosomeSequence> chromosomeSequences)
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static LinkedHashMap<String,ChromosomeSequence> |
loadFastaAddGeneFeaturesFromGeneIDGFF2(File fastaSequenceFile,
File gffFile)
Loads Fasta file and GFF2 feature file generated from the geneid prediction algorithm |
static LinkedHashMap<String,ChromosomeSequence> |
loadFastaAddGeneFeaturesFromGeneMarkGTF(File fastaSequenceFile,
File gffFile)
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static LinkedHashMap<String,ChromosomeSequence> |
loadFastaAddGeneFeaturesFromGlimmerGFF3(File fastaSequenceFile,
File gffFile)
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static LinkedHashMap<String,ChromosomeSequence> |
loadFastaAddGeneFeaturesFromGmodGFF3(File fastaSequenceFile,
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 LinkedHashMap<String,ChromosomeSequence> |
loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(File fastaSequenceFile,
File uppercaseFastaFile,
boolean throwExceptionGeneNotFound)
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static void |
main(String[] args)
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static void |
outputFastaSequenceLengthGFF3(File fastaSequenceFile,
File gffFile)
Output a gff3 feature file that will give the length of each scaffold/chromosome in the fasta file. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public GeneFeatureHelper()
Method Detail |
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public static LinkedHashMap<String,ChromosomeSequence> loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(File fastaSequenceFile, File uppercaseFastaFile, boolean throwExceptionGeneNotFound) throws Exception
Exception
public static void outputFastaSequenceLengthGFF3(File fastaSequenceFile, File gffFile) throws Exception
fastaSequenceFile
- gffFile
-
Exception
public static LinkedHashMap<String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGeneIDGFF2(File fastaSequenceFile, File gffFile) throws Exception
fastaSequenceFile
- gffFile
-
Exception
public static void addGeneIDGFF2GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws Exception
chromosomeSequenceList
- listGenes
-
Exception
public static LinkedHashMap<String,ChromosomeSequence> getChromosomeSequenceFromDNASequence(LinkedHashMap<String,DNASequence> dnaSequenceList)
public static LinkedHashMap<String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGmodGFF3(File fastaSequenceFile, File gffFile, boolean lazyloadsequences) throws 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 memory
Exception
public static void addGmodGFF3GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws Exception
chromosomeSequenceList
- listGenes
-
Exception
public static LinkedHashMap<String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGlimmerGFF3(File fastaSequenceFile, File gffFile) throws Exception
Exception
public static void addGlimmerGFF3GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws Exception
Exception
public static LinkedHashMap<String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGeneMarkGTF(File fastaSequenceFile, File gffFile) throws Exception
Exception
public static void addGeneMarkGTFGeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws Exception
Exception
public static LinkedHashMap<String,ProteinSequence> getProteinSequences(Collection<ChromosomeSequence> chromosomeSequences) throws Exception
Exception
public static LinkedHashMap<String,GeneSequence> getGeneSequences(Collection<ChromosomeSequence> chromosomeSequences) throws Exception
Exception
public static void main(String[] args) throws Exception
Exception
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