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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
package examples;
import ngs.ErrorMsg;
import ngs.ReadCollection;
import ngs.Reference;
import ngs.ReferenceIterator;
public class DumpReferenceFASTA
{
private static void process ( Reference ref )
throws ErrorMsg
{
long len = ref . getLength ();
int line = 0;
System.out.println ( ">" + ref . getCanonicalName () );
try
{
for ( long offset = 0; offset < len; offset += 5000 )
{
String chunk = ref . getReferenceChunk ( offset, 5000 );
int chunk_len = chunk . length ();
for ( int chunk_idx = 0; chunk_idx < chunk_len; )
{
int endIndex = chunk_idx + 70 - line;
if ( endIndex > chunk_len )
endIndex = chunk_len;
String chunk_line
= chunk . substring ( chunk_idx, endIndex );
line += chunk_line . length ();
chunk_idx += chunk_line . length ();
System.out.print ( chunk_line );
if ( line >= 70 )
{
System.out.println ();
line = 0;
}
}
}
}
catch ( ErrorMsg x )
{
}
}
private static void run ( ReadCollection run, String reference )
throws ErrorMsg
{
Reference ref = run . getReference ( reference );
process ( ref );
}
private static void run ( ReadCollection run )
throws ErrorMsg
{
ReferenceIterator refs = run . getReferences ();
while ( refs . nextReference () )
{
process ( refs );
System.out.println();
}
}
public static void main ( String [] args )
{
boolean failure = true;
if ( args.length < 1 || args.length > 2 )
{
System.out.print
( "Usage: DumpReferenceFASTA accession [ reference ]\n" );
}
else try
{
String acc = args[0];
// open requested accession using SRA implementation of the API
ReadCollection run
= gov.nih.nlm.ncbi.ngs.NGS.openReadCollection ( acc );
if ( args.length == 2 )
run ( run, args[1] );
else
run ( run );
failure = false;
}
catch ( ErrorMsg x )
{
System.err.println ( x.toString () );
x.printStackTrace ();
}
catch ( Exception x )
{
System.err.println ( x.toString () );
x.printStackTrace ();
}
if ( failure)
System.exit ( 10 );
}
}
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