import java.util.*;
import javagene.seq.*;
import javagene.io.*;
import javagene.util.*;
/**
*
* Get the translated protein sequence for each of the
* genes in a GFF file.
*
* Illustrates reading of Fasta and GFF files, selection
* of features that have specific attributes, splicing,
* translation into protein sequence.
*
*/
public class GenesToProteins
{
public static void main( String[] args )
throws Exception
{
//
// First read the sample Fasta file into a sequence object.
//
// The 20000 parameter is a hint to the read() method to
// expect a sequence of around this size.
//
// This sequence is a portion of human chr21
//
// NOTE - you may need to edit this filepath, depending on where
// you installed the javagene.jar file and samples!
//
SeqI seqRaw= Fasta.read( "./sample/sample.fa", 20000 );
//
// Since the genomic location and type of the sequence are
// not in the Fasta file, we have to add this information here
// and create a SeqStranded object.
// (yes, sorry, I know this step is confusing...)
SeqI seqChr21Portion= new SeqStranded( seqRaw,
Location.fromBio( 36457709, 39608421, '+' ),
Nucleotide.Type.DNA );
//
// Now read in a GTF file full of "features".
//
// This sample file contains features describing known genes in our sequence.
//
FeatureList listChr21Genes= Gff.read( "./sample/sample.gtf" );
//
// Get a list of the genes in the GTF file:
// attributeValues() returns a collection of all the values found for
// the specified attribute key; in this case, the "gene_id" key of a GTF feature.
Collection<String> geneIds= listChr21Genes.attributeValues( "gene_id" );
//
// We want to show the proteins that are coded
// so iterate over this collection of gene ids.
for( String gene: geneIds )
{
// we want the translated protein residues for each gene...
// get all the individual features (exons, CDS regions, etc.) of this gene
FeatureList listGene= listChr21Genes.selectByAttribute( "gene_id", gene );
// now select only the coding regions of this gene
listGene= listGene.selectByType( "CDS" );
// sort them
listGene= listGene.sortByStart();
// splice them together
String codingRegion= listGene.splice( seqChr21Portion );
// all of the above statements could have been chained, like so:
// codingRegion= listChr21Genes.selectByAttribute( "gene_id", gene ).selectByType( "CDS" ).sortByStart().splice( seqChr21Portion );
// translate them
String protein= AminoAcid.translate( codingRegion );
// show translations on screen
Log.log( gene + "= " + protein );
Log.log();
}
}
}
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