Class GeneFeatureHelper

Method Details

• loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile

  public static LinkedHashMap<String,ChromosomeSequence> loadFastaAddGeneFeaturesFromUpperCaseExonFastaFile(File fastaSequenceFile, File uppercaseFastaFile, boolean throwExceptionGeneNotFound) throws Exception

  Throws:

  Exception

• outputFastaSequenceLengthGFF3

  public static void outputFastaSequenceLengthGFF3(File fastaSequenceFile, File gffFile) throws 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:

  Exception

• loadFastaAddGeneFeaturesFromGeneIDGFF2

  public static LinkedHashMap<String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGeneIDGFF2(File fastaSequenceFile, File gffFile) throws Exception

  Loads Fasta file and GFF2 feature file generated from the geneid prediction algorithm

  Parameters:

  fastaSequenceFile -

  gffFile -

  Returns:

  Throws:

  Exception

• addGeneIDGFF2GeneFeatures

  public static void addGeneIDGFF2GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws Exception

  Load GFF2 feature file generated from the geneid prediction algorithm and map features onto the chromosome sequences

  Parameters:

  chromosomeSequenceList -

  listGenes -

  Throws:

  Exception

• getChromosomeSequenceFromDNASequence

  public static LinkedHashMap<String,ChromosomeSequence> getChromosomeSequenceFromDNASequence(LinkedHashMap<String,DNASequence> dnaSequenceList)

• loadFastaAddGeneFeaturesFromGmodGFF3

  public static LinkedHashMap<String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGmodGFF3(File fastaSequenceFile, File gffFile, boolean lazyloadsequences) throws 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:

  Exception

• addGmodGFF3GeneFeatures

  public static void addGmodGFF3GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws Exception

  Load GFF3 file using mRNA as the gene feature as not all GFF3 files are complete

  Parameters:

  chromosomeSequenceList -

  listGenes -

  Throws:

  Exception

• loadFastaAddGeneFeaturesFromGlimmerGFF3

  public static LinkedHashMap<String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGlimmerGFF3(File fastaSequenceFile, File gffFile) throws Exception

  Throws:

  Exception

• addGlimmerGFF3GeneFeatures

  public static void addGlimmerGFF3GeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws Exception

  Throws:

  Exception

• loadFastaAddGeneFeaturesFromGeneMarkGTF

  public static LinkedHashMap<String,ChromosomeSequence> loadFastaAddGeneFeaturesFromGeneMarkGTF(File fastaSequenceFile, File gffFile) throws Exception

  Throws:

  Exception

• addGeneMarkGTFGeneFeatures

  public static void addGeneMarkGTFGeneFeatures(LinkedHashMap<String,ChromosomeSequence> chromosomeSequenceList, FeatureList listGenes) throws Exception

  Throws:

  Exception

• getProteinSequences

  public static LinkedHashMap<String,ProteinSequence> getProteinSequences(Collection<ChromosomeSequence> chromosomeSequences) throws Exception

  Throws:

  Exception

• getGeneSequences

  public static LinkedHashMap<String,GeneSequence> getGeneSequences(Collection<ChromosomeSequence> chromosomeSequences) throws Exception

  Throws:

  Exception

• main

  public static void main(String[] args) throws Exception

  Throws:

  Exception