/usr/bin/bp_classify_hits_kingdom is in bioperl 1.6.924-3.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 | #!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
=head1 NAME
bp_classify_hits_kingdom - classify BLAST hits by taxonomic kingdom
=head2 USAGE
bp_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]
=head2 DESCRIPTION
Will print out the taxonomic distribution (at the kingdom level) for a
set of hits against the NR database. By default, this script assumes you
did a search against the protein database (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 File path of the gi2taxid file (gi_taxid_prot.dmp for proteins
or gi_taxid_nucl.dmp if the search was against a nucleid database)
-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 created in your directory after
making these changes.
=head2 AUTHOR
Jason Stajich jason_at_bioperl_dot_org
=cut
use strict;
use warnings;
use Bio::DB::Taxonomy;
use DBI;
use Env;
use File::Spec;
use vars qw($SEP);
my $DEBUG = 0;
use Getopt::Long;
$SEP = '_';
my $evalue_filter = 1e-3;
my @files;
my $zcat = 'zcat'; # or gunzip -c
my $prefix = File::Spec->catfile($HOME,'taxonomy');
my $gi2taxidfile = "$prefix/gi_taxid_prot.dmp.gz";
my $force = 0; # don't use the cached gi2taxid file
GetOptions(
'v|verbose|debug' => \$DEBUG,
'force!' => \$force,
'z|zcat:s' => \$zcat,
'i|in:s' => \@files,
'e|evalue:f' => \$evalue_filter,
't|taxonomy:s' => \$prefix,
'g|gi|gi2taxid:s' => \$gi2taxidfile,
'h|help' => sub { system('perldoc', $0); exit },
);
# insure idx location is created
mkdir(File::Spec->catfile($prefix,'idx'))
unless -d File::Spec->catfile($prefix,'idx');
# these files came from ftp://ftp.ncbi.nih.gov/pub/taxonomy
my $taxdb = Bio::DB::Taxonomy->new
(-source => 'flatfile',
-directory => File::Spec->catfile
($prefix, 'idx'),
-nodesfile => File::Spec->catfile($prefix,'nodes.dmp'),
-namesfile => File::Spec->catfile($prefix,'names.dmp')
);
my %query;
my (%taxid4gi,%gi2node);
my $dbh = tie(%gi2node, 'DB_File', 'gi2class');
my $giidxfile = File::Spec->catfile($prefix,'idx','gi2taxid');
my $done = -f $giidxfile;
$done = 0 if $force;
my $dbh2 = $dbh = DBI->connect("dbi:SQLite:dbname=$giidxfile","","");
if( ! $done ) {
$dbh2->do("CREATE TABLE gi2taxid ( gi integer PRIMARY KEY,
taxid integer NOT NULL)");
$dbh2->{AutoCommit} = 0;
my $fh;
# this file came from ftp://ftp.ncbi.nih.gov/pub/taxonomy
# I'm interested in protein hits therefor _prot file.
if (not -f $gi2taxidfile) {
die "Error: File $gi2taxidfile does not exist\n";
}
if( $gi2taxidfile =~ /\.gz$/ ) {
open($fh, "$zcat $gi2taxidfile |" ) || die "$zcat $gi2taxidfile: $!";
} else {
open($fh, $gi2taxidfile ) || die "Error: could not read file $gi2taxidfile: $!";
}
my $i = 0;
my $sth = $dbh2->prepare("INSERT INTO gi2taxid (gi,taxid) VALUES (?,?)");
while(<$fh>) {
my ($gi,$taxid) = split;
$sth->execute($gi,$taxid);
$i++;
if( $i % 500000 == 0 ) {
$dbh->commit;
warn("$i\n") if $DEBUG;
}
}
$dbh->commit;
$sth->finish;
}
for my $file ( @files ) {
warn("$file\n");
my $gz;
if( $file =~ /\.gz$/) {
$gz = 1;
}
my ($spname) = split(/\./,$file);
my ($fh,$i);
if( $gz ) {
open($fh, "$zcat $file |") || die "$zcat $file: $!";
} else {
open($fh, $file) || die "$file: $!";
}
my $sth = $dbh->prepare("SELECT taxid from gi2taxid WHERE gi=?");
while(<$fh>) {
next if /^\#/;
my ($qname,$hname,$pid,$qaln,$mismatch,$gaps,
$qstart,$qend,$hstart,$hend,
$evalue,$bits,$score) = split(/\t/,$_);
next if( $evalue > $evalue_filter );
if( ! exists $query{$spname}->{$qname} ) {
$query{$spname}->{$qname} = {};
}
if( $hname =~ /gi\|(\d+)/) {
my $gi = $1;
if( ! $gi2node{$gi} ){ # see if we cached the results from before
$sth->execute($gi);
my $taxid;
$sth->bind_columns(\$taxid);
if( ! $sth->fetch ) {
warn("no taxid for $gi\n");
next;
}
my $node = $taxdb->get_Taxonomy_Node($taxid);
if( ! $node ) {
warn("cannot find node for gi=$gi ($hname) (taxid=$taxid)\n");
next;
}
my $parent = $taxdb->get_Taxonomy_Node($node->parent_id);
# THIS IS WHERE THE KINGDOM DECISION IS MADE
# DON'T FORGET TO WIPE OUT YOUR CACHE FILE
# gi2class after you make changes here
while( defined $parent && $parent->node_name ne 'root' ) {
# this is walking up the taxonomy hierarchy
# can be a little slow, but works...
#warn( "\t",$parent->rank, " ", $parent->node_name, "\n");
# deal with Eubacteria, Archea separate from
# Metazoa, Fungi, Viriplantae differently
# (everything else Eukaryotic goes in Eukaryota)
if( $parent->rank eq 'kingdom') {
# caching in ...
($gi2node{$gi}) = $parent->node_name;
last;
} elsif( $parent->rank eq 'superkingdom' ) {
# caching in ...
($gi2node{$gi}) = $parent->node_name;
$gi2node{$gi} =~ s/ \<(bacteria|archaea)\>//g;
last;
}
$parent = $taxdb->get_Taxonomy_Node($parent->parent_id);
}
}
my ($kingdom) = $gi2node{$gi};
#warn("$gi2node{$gi}\n");
unless( defined $kingdom && length($kingdom) ) {
#warn("no kingdom for $hname\n");
} else {
$query{$spname}->{$qname}->{$kingdom}++;
}
} else {
warn("no GI in $hname\n");
}
}
last if ( $DEBUG && $i++ > 10000);
$sth->finish;
}
# print out the taxonomic distribution
while( my ($sp,$d) = each %query ) {
my $total = scalar keys %$d;
print "$sp total=$total\n";
my %seen;
for my $v ( values %$d ) {
my $tag = join(",",sort keys %$v );
$seen{$tag}++;
}
for my $t ( sort { $seen{$a} <=> $seen{$b} } keys %seen ) {
printf " %-20s\t%d\t%.2f%%\n",
$t,$seen{$t}, 100 * $seen{$t} / $total;
}
print "\n\n";
}
|