org.irisa.genouest.logol.utils.converter
Class GFFConverter
java.lang.Object
org.irisa.genouest.logol.utils.converter.GFFConverter
public class GFFConverter
- extends java.lang.Object
History:
Fix 1659 O. Sallou 21/07/10: GFF output should start at position 1, add 1 to positions
- Author:
- osallou
Method Summary |
void |
convert2GFF(java.lang.String inputFile,
java.lang.String outputFile)
Read fasta file from results, load seq name from file
Size will be min/max of matches |
static void |
main(java.lang.String[] args)
GFF converter from Logol result file |
void |
writeGFF(java.lang.String outputFile,
org.biojava.bio.program.gff.GFFEntrySet gffSet)
|
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
GFFConverter
public GFFConverter()
main
public static void main(java.lang.String[] args)
- GFF converter from Logol result file
- Parameters:
args
- input and output file
writeGFF
public void writeGFF(java.lang.String outputFile,
org.biojava.bio.program.gff.GFFEntrySet gffSet)
throws java.io.IOException
- Throws:
java.io.IOException
convert2GFF
public void convert2GFF(java.lang.String inputFile,
java.lang.String outputFile)
throws java.util.NoSuchElementException
- Read fasta file from results, load seq name from file
Size will be min/max of matches
- Parameters:
inputFile
- File of matches for a sequenceoutputFile
- File to write the GFF
- Throws:
java.util.NoSuchElementException
org.biojava.bio.BioException