1BP_CLASSIFY_HITS_KINGDOUMs(e1r)Contributed Perl DocumentBaPt_iCoLnASSIFY_HITS_KINGDOM(1)
2
3
4

NAME

6       classify_hits_kingdom - classify BLAST hits by taxonomic kingdom
7
8       USAGE
9
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]
14
15       DESCRIPTION
16
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.
21
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).
25
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.
32
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
39
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.
48
49       AUTHOR
50
51       Jason Stajich jason_at_bioperl_dot_org
52
53
54
55perl v5.8.8                       2007-05-07       BP_CLASSIFY_HITS_KINGDOM(1)
Impressum