org.nmdp.ngs.align

Class Genewise

java.lang.Object

org.nmdp.ngs.align.Genewise

public final class Genewise
extends Object

Utility to run genewise via the command line.

Method Summary

Methods

Modifier and Type	Method and Description
static Iterable<GenewiseExon>	genewiseExons(File aminoAcidHmm2File, File genomicDnaFastaFile) Return the exons predicted from the alignment of the specified amino acid HMM file in HMMER2 format against the specified genomic DNA sequence file in FASTA format.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

genewiseExons

public static Iterable<GenewiseExon> genewiseExons(File aminoAcidHmm2File,
                                   File genomicDnaFastaFile)
                                            throws IOException

Return the exons predicted from the alignment of the specified amino acid HMM file in HMMER2 format against the specified genomic DNA sequence file in FASTA format.

Parameters:

aminoAcidHmm2File - amino acid HMM file in HMMER2 format, must not be null

genomicDnaFastaFile - genomic DNA sequence file in FASTA format, must not be null

Returns:

zero or more exons predicted from the alignment of the specified amino acid HMM file in HMMER2 format against the specified genomic DNA sequence file in FASTA format

Throws:

IOException - if an I/O error occurs