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bp_classify_hits_kingdom - classify BLAST hits by taxonomic kingdom

bp_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. 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 FASTA).

Input values:
-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.

Jason Stajich jason_at_bioperl_dot_org

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