BP_CLASSIFY_HITS_KINGDUser)Contributed Perl DocumenBP_CLASSIFY_HITS_KINGDOM(1)NAME
classify_hits_kingdom - classify BLAST hits by taxonomic kingdom
USAGE
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]
DESCRIPTION
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 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 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
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.
Flags
-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.
AUTHOR
Jason Stajich jason_at_bioperl_dot_org
perl v5.14.1 2011-07-22 BP_CLASSIFY_HITS_KINGDOM(1)
