Using BioJava to Parsing FASTA 使用 BioJAVA 讀取 FASTA 檔案

Introudce

簡介

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One of methods to parse FASTA in BioJava cookbook is using SeqIOTools which has been marked as deprecated.

BioJava 上的 Cookbook 範例有讀取 FASTA 的教學，不過所使用的 API "SeqIOTools" 在 Docs 上已經被標註為 Deprecated。

So, this example shows how to do it in other ways, like SequenceIterator and RichSequence.

因此以下的 Code 除了舊式寫法外，還包含了使用 SequenceIterator 以及 RichSequence 來達成

 

 

 

Code

原始碼

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import java.io.*;

import java.util.*;

import org.biojava.bio.*;

import org.biojava.bio.seq.*;

import org.biojava.bio.seq.db.*;

import org.biojava.bio.seq.io.*;

import org.biojava.bio.symbol.*;

import org.biojavax.bio.seq.RichSequence;

import org.biojavax.bio.seq.RichSequenceIterator;

public class ReadFasta {

  /**

   *  This is sample code for parsing FASTA by using BioJava 

   * 本程式測試如何使用 BioJava 取得 FASTA 序列並輸出

   */

  public static void main(String[] args) throws IOException, BioException {

    try {

 

      /* set up parameters

       * 設定必要參數 

       */

      String sFilename = "D:\\working\\cRAP_200905_prefixCON.fasta";

      String sSeqType="PROTEIN";

      String sFileType="FASTA";

 

      /* for Sequence DB

       * 給 SequenceDB 使用

       */

      BufferedInputStream is = new BufferedInputStream(new FileInputStream(sFilename));      

 

      /* for Sequence Iterator 

       * 給 SequenceIterator 與 RichSequenceIterator 使用

       */

      BufferedReader br = new BufferedReader(new FileReader(sFilename));         

 

      /* for SequenceDB 

       * 給 SequenceDB 使用

       */

      Alphabet alpha = AlphabetManager.alphabetForName(sSeqType);  

      /*  Parsing FASTA by SeqIOTools (Deprecated)

       *  使用舊型 SeqIOTools 來取得(已棄置)
       */

      /* get a SequenceDB of all sequences in the file

       * 使用 SequenceDB 方式取得: 會有序列不按照順序的問題

       */
      //SequenceDB db =  SeqIOTools.readFasta(is, alpha);
      //SeqIOTools.writeFasta(System.out, db);
      /*  Test method of Sequence

       *  測試 Sequence 的 method

       */
      //System.out.println("getClass: "+db.getClass());
      //System.out.println("ids: "+db.ids());
      //System.out.println("getName: "+db.getName());
      //System.out.println("getSequence: "+db.getSequence("CON_sp|ALBU_BOVIN|").seqString());
      //SeqIOTools.writeFasta(System.out, db);
     
      /* Parsing FASTA by SequenceIterator

       * 使用 SequenceIterator 方式取得       

       */
      SequenceIterator iter =(SequenceIterator) SeqIOTools.fileToBiojava(sFileType, sSeqType,br);

       /*
       int iCount=0;
       while (  iter.hasNext()  ){
          Sequence s = iter.nextSequence();

          //String name = s.getName();
          //s.length();
          //s.getAnnotation();
          System.out.println("\nName: "+s.getName());
          System.out.println("\tAnnotation: "+s.getAnnotation());
          System.out.println("\tSeq: "+s.seqString());
          iCount++;
         
        }
        System.out.println("\tCount for Seq: "+iCount);
       */

      /*  Parsing FASTA by RichSequence

       * 使用新的 RichSequence 方式來取得:

       */

       RichSequenceIterator rsIter = RichSequence.IOTools.readFastaProtein(br, null);

       while (rsIter.hasNext()){

          RichSequence rsSequence = rsIter.nextRichSequence();

          //String name = s.getName();

          //s.length();

          //s.getAnnotation();

          System.out.println("\tAccession: "+rsSequence.getAccession());

          System.out.println("\tDescription: "+rsSequence.getDescription());

          System.out.println("\tDivision: "+rsSequence.getDivision());

          System.out.println("\tName: "+rsSequence.getName());

          System.out.println("\tseqString: "+rsSequence.seqString());

      

       }

     

    }

    catch (BioException ex) {

      //not in fasta format or wrong alphabet

      ex.printStackTrace();

    }catch (NoSuchElementException ex) {

      //no fasta sequences in the file

      ex.printStackTrace();

    }catch (FileNotFoundException ex) {

      //problem reading file

      ex.printStackTrace();

    }

  }

}

 

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Reference 

參考

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Parsing FASTA by SeqIOTools

使用舊型的 SeqIOTools 來取得 FASTA 範例

http://www.biojava.org/wiki/BioJava:Cookbook:SeqIO:ReadFasta

Parsing FASTA by RichSequence

RichSequence.IOTools 的 API

http://www.biojava.org/docs/api/org/biojavax/bio/seq/RichSequence.IOTools.html