1BP_CLASSIFY_HITS_KINGDOUMs(e1r)Contributed Perl DocumentBaPt_iCoLnASSIFY_HITS_KINGDOM(1)
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NAME

6       classify_hits_kingdom - classify BLAST hits by taxonomic kingdom
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8   USAGE
9       classify_hits_kingdom [-i tab_file] [-i second_BLAST_file] [-e
10       evalue_cutoff]
11                             [-t dir_where_TAXONOMY_files_are] [-g gi2taxid]
12                             [-z PATH_TO_zcat] [-v]
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14   DESCRIPTION
15       Will print out the taxonomic distribution (at the kingdom level) for a
16       set of hits against the NR database.  This script assumes you've done a
17       search against the protein database, you'll have to make minor changes
18       in the gi_taxid part to point to the gi_taxid_nuc.dump file.
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20       This expects BLAST files in tabbed -m9 or -m8 format.  Output with -m 8
21       or use blast2table.pl to convert (or fastam9_to_table.PLS if using
22       FASTA).
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24         Input values:
25          -t/--taxonomy  directory where the taxonomy .dmp files are (from NCBI)
26          -g/--gi        Location of gi_taxid_prot.dmp (or gi_taxid_nucl.dmp if
27                         the search was against a NT db)
28          -i/--in        The name of the tab delimited -m8/-m9 output files to
29                         process.
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31           -e/--evalue   Provide an E-value cutoff for hits to be considered
32           -z/--zcat     Path to the 'zcat' executable, can also be 'gunzip -c'
33                         if no zcat on your system.
34          Flags
35           -v/--verbose  To turn on verbose messages
36           -h/--help     Display this helpful information
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38       This is intended to be useful starting script, but users may want to
39       customize the output and parameters.  Note that I am summarizing the
40       kingdoms here and Eukaryota not falling into Metazoa, Viridiplantae, or
41       Fungi gets grouped into the general superkingdom Eukaryota. for
42       simplicity.  There are comments in the code directing you to where
43       changes can be made if you wanted to display hits by phylum for
44       example.  Note that you must wipe out the cache file 'gi2class' that is
45       craeed in your directory after making these changes.
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47   AUTHOR
48       Jason Stajich jason_at_bioperl_dot_org
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52perl v5.12.0                      2010-04-29       BP_CLASSIFY_HITS_KINGDOM(1)
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