Annotations:List
How do I List the Annotations in a Sequence?
When you read in a annotates sequence file such as GenBank or EMBL there is a lot more detailed information in there than just the raw sequence. If the information has a sensible location then it ends up as a Feature. If it is more generic such as the species name then the information ends up as Annotations.
BioJava Annotation objects are a bit like Map objects and they contian key value mappings.
Below is the initial portion of an EMBL file
ID AY130859 standard; DNA; HUM; 44226 BP.
XX
AC AY130859;
XX
SV AY130859.1
XX
DT 25-JUL-2002 (Rel. 72, Created)
DT 25-JUL-2002 (Rel. 72, Last updated, Version 1)
XX
DE Homo sapiens cyclin-dependent kinase 7 (CDK7) gene, complete cds.
XX
KW .
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN [1]
RP 1-44226
RA Rieder M.J., Livingston R.J., Braun A.C., Montoya M.A., Chung M.-W.,
RA Miyamoto K.E., Nguyen C.P., Nguyen D.A., Poel C.L., Robertson P.D.,
RA Schackwitz W.S., Sherwood J.K., Witrak L.A., Nickerson D.A.;
RT ;
RL Submitted (11-JUL-2002) to the EMBL/GenBank/DDBJ databases.
RL Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, WA
RL 98195, USA
XX
CC To cite this work please use: NIEHS-SNPs, Environmental Genome
CC Project, NIEHS ES15478, Department of Genome Sciences, Seattle, WA
CC (URL: http://egp.gs.washington.edu).
The following program reads an EMBL file and lists its Annotation properties. The output of this program on the above file is listed below the program.
```java import java.io.*; import java.util.*;
import org.biojava.bio.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.io.*;
public class ListAnnotations {
public static void main(String[] args) {
try {
//read in an EMBL Record
BufferedReader br = new BufferedReader(new FileReader(args[0]));
//for each sequence list the annotations
for(SequenceIterator seqs = SeqIOTools.readEmbl(br); seqs.hasNext(); ){
Annotation anno = seqs.nextSequence().getAnnotation();
//print each key value pair
for (Iterator i = anno.keys().iterator(); i.hasNext(); ) {
Object key = i.next();
System.out.println(key +" : "+ anno.getProperty(key));
}
}
}
catch (Exception ex) {
ex.printStackTrace();
}
}
} ```
Program Output
RN : [1]
KW : .
RL : [Submitted (11-JUL-2002) to the EMBL/GenBank/DDBJ databases., Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, WA, 98195, USA]
embl_accessions : [AY130859]
DE : Homo sapiens cyclin-dependent kinase 7 (CDK7) gene, complete cds.
SV : AY130859.1
AC : AY130859;
FH : Key Location/Qualifiers
XX :
OC : [Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;, Eutheria; Primates; Catarrhini; Hominidae; Homo.]
RA : [Rieder M.J., Livingston R.J., Braun A.C., Montoya M.A., Chung M.-W.,, Miyamoto K.E., Nguyen C.P., Nguyen D.A., Poel C.L., Robertson P.D.,, Schackwitz W.S., Sherwood J.K., Witrak L.A., Nickerson D.A.;]
ID : AY130859 standard; DNA; HUM; 44226 BP.
DT : [25-JUL-2002 (Rel. 72, Created), 25-JUL-2002 (Rel. 72, Last updated, Version 1)]
CC : [To cite this work please use: NIEHS-SNPs, Environmental Genome, Project, NIEHS ES15478, Department of Genome Sciences, Seattle, WA, (URL: http://egp.gs.washington.edu).]
RT : ;
OS : Homo sapiens (human)
RP : 1-44226