Package bacnet.scripts.listeriomics

Class PhylogenyListeriomics

java.lang.Object
bacnet.scripts.listeriomics.PhylogenyListeriomics
public class PhylogenyListeriomics extends Object
Different methods to create phylogeny tree, and tables for each genome elements
Author:
UIBC

  • Field Details

    • PATH

      public static String PATH

    • LOCUSTAG_CHANGE_PATH

      public static String LOCUSTAG_CHANGE_PATH

    • NOTFOUND_LOCUSTAG_CHANGE_PATH

      public static String NOTFOUND_LOCUSTAG_CHANGE_PATH

    • bigDataset

      public static String bigDataset

  • Constructor Details

    • PhylogenyListeriomics

      public PhylogenyListeriomics()

  • Method Details

    • run

      public static void run()

    • searchMissingLocus

      public static void searchMissingLocus()
      By going through all GFF available search for the corresponding locustag

    • parseData

      public static void parseData()
      Using LOCUSTAG_CHANGE_PATH modify every table by changin locutag ID or removing the row if the gene is not found

    • transformData

      public static boolean transformData()
      For each genome save a list of genes and their homologs

    • getAlllocusTagINRA

      public static void getAlllocusTagINRA()

    • getAlllocusTag

      public static void getAlllocusTag()

    • getAlllocusTagFromGFF

      public static void getAlllocusTagFromGFF()
      They used old_locus_tag for the conservation analysis, so we need to create a HashMap to have the equivalent GeneId old_locus_tag ---> locus_tag in the GFF

    • findLocusTag

      public static void findLocusTag(String locus)

    • findLocusTag

      public static String findLocusTag(String locus, String genomeName)
      Search a locustag in all GFF present for a genomeName
      Parameters:
      locus -
      genomeName -

    • cleanSVGFile

      public static void cleanSVGFile()
      Clean SVG file to be able to replace strain name by homolog information
      Names of strain are created in many different "Text table" in the SVG file which have to be removed

    • addPhylogenyToGenes

      public static void addPhylogenyToGenes()
      Go through all result files and create Conservation HadhMap for each Gene

    • getGenomes

      public static void getGenomes()
      get the list of genome IDs and corresponding genome Names
      And verify if all genomes are here!