static public LinkedHashMap < String , ChromosomeSequence > loadFastaAddGeneFeaturesFromGeneIDGFF2 ( File fastaSequenceFile , File gffFile ) throws Exception { LinkedHashMap < String , DNASequence > dnaSequenceList = FastaReaderHelper . readFastaDNASequence ( fastaSequenceFile ) ; LinkedHashMap < String , ChromosomeSequence > chromosomeSequenceList = GeneFeatureHelper . getChromosomeSequenceFromDNASequence ( dnaSequenceList ) ; FeatureList listGenes = GeneIDGFF2Reader . read ( gffFile . getAbsolutePath ( ) ) ; addGeneIDGFF2GeneFeatures ( chromosomeSequenceList , listGenes ) ; return chromosomeSequenceList ; }
Loads Fasta file and GFF2 feature file generated from the geneid prediction algorithm