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import java.io.File; |
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import java.io.FileNotFoundException; |
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import java.io.IOException; |
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import java.io.PrintStream; |
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|
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import owl.core.sequence.alignment.AlignmentConstructionException; |
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import owl.core.sequence.alignment.MultipleSequenceAlignment; |
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import owl.core.util.FileFormatException; |
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|
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public class pir2fasta { |
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|
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/*------------------------------ constants ------------------------------*/ |
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|
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/** |
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* To read a input file in pir format and write to a output file or stdout in fasta format |
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* @param args |
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*/ |
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public static void main(String[] args) { |
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|
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if(args.length < 1 || args.length > 2) { |
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System.out.println("Usage: pir2fasta input.pir [output.fa]"); |
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System.exit(1); |
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} |
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|
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String inputfilename = args[0]; |
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String outputfilename = null; |
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|
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if(!new File(inputfilename).canRead()) { |
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System.err.println("Error: Could not read from file " + inputfilename); |
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System.exit(1); |
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} |
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|
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PrintStream ps = System.out; |
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|
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if (args.length == 2){ |
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outputfilename = args[1]; |
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try { |
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ps = new PrintStream(outputfilename); |
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} catch (FileNotFoundException e1) { |
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System.out.println("Failed to open file " + outputfilename + ": " + e1.getMessage()); |
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System.exit(1); |
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} |
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} |
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|
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|
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//create a multiple sequence alignment from the input pir file |
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MultipleSequenceAlignment ma = null; |
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try { |
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ma = new MultipleSequenceAlignment(inputfilename, MultipleSequenceAlignment.PIRFORMAT); |
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ma.writeFasta(ps, 80, true); |
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if(outputfilename != null) { |
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System.out.println(inputfilename + " -> " + outputfilename); |
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} |
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} catch (IOException e) { |
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System.err.println("Error while processing " + inputfilename + ": " + e.getMessage()); |
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} catch (FileFormatException e) { |
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System.err.println("Invalid format of " + inputfilename + ": " + e.getMessage()); |
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} catch (AlignmentConstructionException e) { |
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System.err.println("Failed to create alignment from file " + inputfilename + ": " + e.getMessage()); |
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} |
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} |
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|
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} |
