Hello,
I compiled a java file and I tried to execute my program to change embl flat
file to ncbi flat file.
But output file(Toncbi.gbk) is o byte.
//ex>java embl_togbk embl_sample
import java.io.*;
import java.util.*;
import java.lang.*;
import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.symbol.*;
public class embl_togbk {
public static void main(String[] args) {
String fileName = args[0];
BufferedReader br;
SequenceIterator seq_iter;
Sequence seq;
try {
br = new BufferedReader(new FileReader(fileName));
seq_iter = SeqIOTools.readEmbl(br);
while(seq_iter.hasNext()) {
seq =seq_iter.nextSequence();
System.out.println(seq.getName());
Iterator feat_iter = seq.features();
while(feat_iter.hasNext()) {
Feature f= (Feature) (feat_iter.next());
Annotation annot = f.getAnnotation();
System.out.println("*+feature: "+
f.getType());
System.out.println();
}
}
// System.out.println();
SeqIOTools.biojavaToFile("GenBank","dna", new
FileOutputStream("Toncbi.gbk"), seq_iter);
br.close();
} catch(Exception e) {
e.printStackTrace();
}
}
}
//-----------------------------------------------
//file:embl_sample
ID A1MVRNA2 standard; DNA; 2593 BP.
XX
AC X01572;
XX
DT 03-AUG-1987 (an correction)
DT 30-JAN-1986 (author review)
DT 17-JUL-1985 (first entry)
XX
DE Alfalfa mosaic virus (A1M4) RNA 2
XX
KW unidentified reading frame.
XX
OS Alfalfa mosaic virus
OC Viridae; ss-RNA nonenveloped viruses; Alfamovirus.
XX
RN [1] (bases 1-2593; enum. 1 to 2593)
RA Cornelissen B.J.C., Brederode F.T., Veeneman G.H., van Boom J.H.,
RA Bol J.F.;
RT "Complete nucleotide sequence of alfalfa mosaic virus RNA 2";
RL Nucl. Acids Res. 11:3019-3025(1983).
XX
CC Data kindly reviewed (30-JAN-1986) by J.F. Bol
XX
FH Key From To Description
FH
FT TRANSCR 1 80 A1MV RNA 2
FT CDS 11 80 unidentified reading frame
XX
SQ Sequence 80 BP; 13 A; 14 C; 21 G; 32 T;
TTTTTTTTTT ATGCCCCCCCC GGGGGGGGGG TTTTTTTTTT TTTTTTTTTT GGGGGGGGGG
AAAAAAAAAA CCCCCCCCTAA
//
-------------------------------------------------------
Is there a problem with this code?
Thank you very much for answer.
Regards.
Jessica
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