Provided by: bioperl_1.6.901-2_all bug


       classify_hits_kingdom - classify BLAST hits by taxonomic kingdom

       classify_hits_kingdom [-i tab_file] [-i second_BLAST_file] [-e evalue_cutoff]
                             [-t dir_where_TAXONOMY_files_are] [-g gi2taxid]
                             [-z PATH_TO_zcat] [-v]

       Will print out the taxonomic distribution (at the kingdom level) for a set of hits against
       the NR database.  This script assumes you've done a search against the protein database,
       you'll have to make minor changes in the gi_taxid part to point to the gi_taxid_nuc.dump

       This expects BLAST files in tabbed -m9 or -m8 format.  Output with -m 8 or use to convert (or fastam9_to_table.PLS if using FASTA).

         Input values:
          -t/--taxonomy  directory where the taxonomy .dmp files are (from NCBI)
          -g/--gi        Location of gi_taxid_prot.dmp (or gi_taxid_nucl.dmp if
                         the search was against a NT db)
          -i/--in        The name of the tab delimited -m8/-m9 output files to

           -e/--evalue   Provide an E-value cutoff for hits to be considered
           -z/--zcat     Path to the 'zcat' executable, can also be 'gunzip -c'
                         if no zcat on your system.
           -v/--verbose  To turn on verbose messages
           -h/--help     Display this helpful information

       This is intended to be useful starting script, but users may want to customize the output
       and parameters.  Note that I am summarizing the kingdoms here and Eukaryota not falling
       into Metazoa, Viridiplantae, or Fungi gets grouped into the general superkingdom
       Eukaryota. for simplicity.  There are comments in the code directing you to where changes
       can be made if you wanted to display hits by phylum for example.  Note that you must wipe
       out the cache file 'gi2class' that is craeed in your directory after making these changes.

       Jason Stajich jason_at_bioperl_dot_org