Package de.julielab.jules.ae.genemapping.resources

Class GeneXMLFromASN1Extractor

  • public class GeneXMLFromASN1Extractor
extends java.lang.Object

    Alternative to GeneXMLDownloader.

    Reads ASN.1 files obtainable from ftp://ftp.ncbi.nih.gov/gene/DATA/ASN_BINARY/ and extracts the required gene information for the JCoRe Gene Mapper.

    This approach is much more robust than downloading everything from the Internet and is most likely also much quicker. However, it relies on an external tool, gene2xml, which is written in C and thus platform dependent. This might cause issues depending on the environment. The available gene2xml programs are located at ftp://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/gene2xml/. The path to the program to use is given as the last parameter when calling this class. This class was used with the linux64 program.

    Author:
    faessler

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void main​(java.lang.String[] args)
      The path to the gene2xml program to use.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • GeneXMLFromASN1Extractor

        public GeneXMLFromASN1Extractor()

    • Method Detail

      • main

        public static void main​(java.lang.String[] args)
                 throws java.lang.Exception
        The path to the gene2xml program to use.
        Throws:
        java.lang.Exception