1BP_CLASSIFY_HITS_KINGDOUMs(e1r)Contributed Perl DocumentBaPt_iCoLnASSIFY_HITS_KINGDOM(1)
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6 classify_hits_kingdom - classify BLAST hits by taxonomic kingdom
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8 USAGE
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10 classify_hits_kingdom [-i tab_file] [-i second_BLAST_file] [-e
11 evalue_cutoff]
12 [-t dir_where_TAXONOMY_files_are] [-g gi2taxid]
13 [-z PATH_TO_zcat] [-v]
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15 DESCRIPTION
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17 Will print out the taxonomic distribution (at the kingdom level) for a
18 set of hits against the NR database. This script assumes you've done a
19 search against the protein database, you'll have to make minor changes
20 in the gi_taxid part to point to the gi_taxid_nuc.dump file.
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22 This expects BLAST files in tabbed -m9 or -m8 format. Output with -m 8
23 or use blast2table.pl to convert (or fastam9_to_table.PLS if using
24 FASTA).
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26 Input values:
27 -t/--taxonomy directory where the taxonomy .dmp files are (from NCBI)
28 -g/--gi Location of gi_taxid_prot.dmp (or gi_taxid_nucl.dmp if
29 the search was against a NT db)
30 -i/--in The name of the tab delimited -m8/-m9 output files to
31 process.
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33 -e/--evalue Provide an E-value cutoff for hits to be considered
34 -z/--zcat Path to the 'zcat' executable, can also be 'gunzip -c'
35 if no zcat on your system.
36 Flags
37 -v/--verbose To turn on verbose messages
38 -h/--help Display this helpful information
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40 This is intended to be useful starting script, but users may want to
41 customize the output and parameters. Note that I am summarizing the
42 kingdoms here and Eukaryota not falling into Metazoa, Viridiplantae, or
43 Fungi gets grouped into the general superkingdom Eukaryota. for sim‐
44 plicity. There are comments in the code directing you to where changes
45 can be made if you wanted to display hits by phylum for example. Note
46 that you must wipe out the cache file 'gi2class' that is craeed in your
47 directory after making these changes.
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49 AUTHOR
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51 Jason Stajich jason_at_bioperl_dot_org
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55perl v5.8.8 2007-05-07 BP_CLASSIFY_HITS_KINGDOM(1)