Class GFF3Reader


  • public class GFF3Reader
    extends java.lang.Object
    http://www.bioperl.org/wiki/GTF Read and write FeatureLists as GFF/GTF formatted files.

    The GFF moniker is applied to a variety of tab-delimited formats that mock the notion of a standard. This class should parse most files bearing at least a passing resemblance to any of the formats. You will, however, need to research the semantics of the files you encounter. Generally, the format consists of 9 tab-delimited fields:
     seqname   source   featureType   start   end   score   strand   frame   attributes
     
    The 9th field consists of key-value pairs separated by semicolons, the first of which JavaGene interprets as the group id (as used in GFF1). It is the precise meaning of this 9th field that varies from week to week. The Feature and FeatureList objects provide various utility methods to ease the task of accessing and using the attributes. The proper interpretation of any particular attribute, however, is left to you.
    Author:
    Hanno Hinsch
    • Constructor Summary

      Constructors 
      Constructor Description
      GFF3Reader()  
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void main​(java.lang.String[] args)  
      static FeatureList read​(java.lang.String filename)  
      static FeatureList read​(java.lang.String filename, java.util.List<java.lang.String> indexes)
      Read a file into a FeatureList.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • GFF3Reader

        public GFF3Reader()
    • Method Detail

      • read

        public static FeatureList read​(java.lang.String filename,
                                       java.util.List<java.lang.String> indexes)
                                throws java.io.IOException
        Read a file into a FeatureList. Each line of the file becomes one Feature object.
        Parameters:
        filename - The path to the GFF file.
        Returns:
        A FeatureList.
        Throws:
        java.io.IOException - Something went wrong -- check exception detail message.
      • read

        public static FeatureList read​(java.lang.String filename)
                                throws java.io.IOException
        Throws:
        java.io.IOException
      • main

        public static void main​(java.lang.String[] args)
                         throws java.lang.Exception
        Throws:
        java.lang.Exception