Will print out the taxonomic distribution (at the kingdom level) for a
set of hits against the NR database. By default, this script assumes you
did a search against the protein database (gi_taxid_nuc.dump file).
This expects BLAST files in tabbed -m9 or -m8 format. Output with -m
8 or use blast2table.pl to convert (or fastam9_to_table.PLS if using
-t/--taxonomy Directory where the taxonomy .dmp files are (from NCBI)
-g/--gi File path of the gi2taxid file (gi_taxid_prot.dmp for proteins
or gi_taxid_nucl.dmp if the search was against a nucleid database)
-i/--in The name of the tab delimited -m8/-m9 output files to process
-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 created in your directory after
making these changes.