X Tutup
Skip to content

Latest commit

 

History

History
119 lines (98 loc) · 4.54 KB

BioJava_CookBook3_Stockholm.md

File metadata and controls

119 lines (98 loc) · 4.54 KB
title permalink
BioJava:CookBook3:Stockholm
wiki/BioJava%3ACookBook3%3AStockholm

How to Read Multiple Sequence Alignment files in Stockholm format

StockholmFileParser is used to read MSA files written in Stockholm file format. This example demonstrates how you can read one or more StockholmStructure object(s) from a Stockholm file.

The StockholmFileParser class can read a single structure object file, a multiple structure objects file, or an InputStream.

To read a single object from a file, you can simply write

public static void main(String[] args){

   try {  
       StockholmFileParser parser = new StockholmFileParser();  
       String pathName= "stockholmFilePathAndName";  
       StockholmStructure structure = parser.parse(pathName);  
             
       //use read structures  
             
   } catch (IOException e) {  
       e.printStackTrace();  
   } catch (Exception e) {  
       e.printStackTrace();  
   }

}

Also you can read multiple alignments within the same file as follows

public static void main(String[] args){

   try {  
       StockholmFileParser parser = new StockholmFileParser();  
       String sourcePath=settingsManager.getSourcePath();  
       String fileName= settingsManager.getFileName();  
       FileInputStream inStream = new FileInputStream(new File(sourcePath,fileName));  
       String outputPath=settingsManager.getOutputPath();  
       parser.parse(inStream,STRUCTURES_TO_SKIP);//if you don't want to start from first structure  
       do {  
           structures = parser.parse(inStream, MAX_PER_ITERATION);  
           for (int i = 0; i < structures.size(); i++) {  
               StockholmStructure structure = structures.get(i);  
               List<AbstractSequence<? extends AbstractCompound>> sequences = structure.getBioSequences(true);  
               final String accessionNumber = structure.getFileAnnotation().getAccessionNumber();  
               final String identification = structure.getFileAnnotation().getIdentification().toString();  
               manageRelatedSequences(accessionNumber, identification,sequences);  
           }  
       } while (structures.size()== MAX_PER_ITERATION);  
   } catch (FileNotFoundException e) {  
       e.printStackTrace();  
   } catch (IOException e) {  
       e.printStackTrace();  
   } catch (Exception e) {  
       e.printStackTrace();  
   }

}

Some times you don't have a reference to the file or input stream

Some times you use the parser in a place other than where it was created.

For example, you can create a StockholmFileParser in a function

   public StockholmFileParser getStockholmFileParser(String filePathName) {  
       StockholmFileParser parser = new StockholmFileParser();  
       try {  
           parser.parse(filePathName, 0);  
       } catch (ParserException e) {  
           e.printStackTrace();  
       } catch (IOException e) {  
           e.printStackTrace();  
       }  
       return parser;  
   }

Then you use the created parser in another function, where you don't have a reference to its underling data source

   public void useParser(StockholmFileParser parser) {  
       final int MAX_PER_ITTERATION = 10;  
       List<StockholmStructure> structures;  
       long count= 0;  
       int successfullyRead = 0;  
       do {  
           try {  
               structures = parser.parseNext(MAX_PER_ITTERATION);  
               successfullyRead = structures.size();  
           } catch (IOException e) {  
               e.printStackTrace();  
           }  
           count += successfullyRead;  
           System.out.println("reached "+count);  
             
           //use read structures  
             
       } while (successfullyRead== MAX_PER_ITTERATION);  
       System.out.println("TOTAL COUNT = "+count);  
   }
X Tutup