1BP_CLASSIFY_HITS_KINGDOUMs(e1r)Contributed Perl DocumentBaPt_iCoLnASSIFY_HITS_KINGDOM(1)
2
3
4
6 classify_hits_kingdom - classify BLAST hits by taxonomic kingdom
7
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]
13
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.
19
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).
23
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.
30
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
37
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.
46
47 AUTHOR
48 Jason Stajich jason_at_bioperl_dot_org
49
50
51
52perl v5.12.0 2010-04-29 BP_CLASSIFY_HITS_KINGDOM(1)