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|
#!/usr/bin/env perl
# Give a Kraken-style report from a Centrifuge output
#
# Based on kraken-report by Derrick Wood
# Copyright 2013-2016, Derrick Wood <dwood@cs.jhu.edu>
#
use strict;
use warnings;
use Getopt::Long;
use File::Basename;
use Cwd;
use Cwd 'cwd' ;
use Cwd 'abs_path' ;
my ($centrifuge_index, $min_score, $min_length);
my $only_unique = 0;
my $show_zeros = 0;
my $is_cnts_table = 0;
my $PROG = "centrifuge-kreport";
my $CWD = dirname( abs_path( $0 ) ) ;
GetOptions(
"help" => \&display_help,
"x=s" => \$centrifuge_index,
"show-zeros" => \$show_zeros,
"is-count-table" => \$is_cnts_table,
"min-score=i" => \$min_score,
"min-length=i"=> \$min_length,
"only-unique" => \$only_unique
) or usage();
usage() unless defined $centrifuge_index;
if (!defined $ARGV[0]) {
print STDERR "Reading centrifuge out file from STDIN ... \n";
}
sub usage {
my $exit_code = @_ ? shift : 64;
print STDERR "
Usage: centrifuge-kreport -x <index name> OPTIONS <centrifuge output file(s)>
centrifuge-kreport creates Kraken-style reports from centrifuge out files.
Options:
-x INDEX (REQUIRED) Centrifuge index
--only-unique Only count reads that were uniquely assigned to one taxon
--show-zeros Show clades that have zero reads, too
--is-count-table The format of the file is 'TAXID<tab>COUNT' instead of the standard
Centrifuge output format
--min-score SCORE Require a minimum score for reads to be counted
--min-length LENGTH Require a minimum alignment length to the read
";
exit $exit_code;
}
sub display_help {
usage(0);
}
my (%child_lists, %name_map, %rank_map);
print STDERR "Loading taxonomy ...\n";
load_taxonomy();
my %taxo_counts;
my $seq_count = 0;
$taxo_counts{0} = 0;
if ($is_cnts_table) {
while (<>) {
my ($taxid,$count) = split;
$taxo_counts{$taxid} = $count;
$seq_count += $count;
}
} else {
my $header = <>;
my @cols = split /\s+/, $header ;
my %headerMap ;
for ( my $i = 0 ; $i < scalar( @cols ) ; ++$i )
{
$headerMap{ $cols[$i] } = $i ;
}
while (<>) {
#my (undef,$seqID,$taxid,$score, undef, $hitLength, $queryLength, $numMatches) = split /\t/;
my @cols = split /\s+/ ;
my $seqID = $cols[ $headerMap{ "seqID" } ] ;
my $taxid = $cols[ $headerMap{ "taxID" } ] ;
my $score = $cols[ $headerMap{ "score" } ] ;
my $hitLength = $cols[ $headerMap{ "hitLength" } ] ;
my $queryLength = $cols[ $headerMap{ "queryLength" } ] ;
my $numMatches = $cols[ $headerMap{ "numMatches" } ] ;
next if $only_unique && $numMatches > 1;
next if defined $min_length && $hitLength < $min_length;
next if defined $min_score && $score < $min_score;
$taxo_counts{$taxid} += 1/$numMatches;
$seq_count++;
}
}
my $classified_count = $seq_count - $taxo_counts{0};
my %clade_counts = %taxo_counts;
dfs_summation(1);
for (keys %name_map) {
$clade_counts{$_} ||= 0;
}
die "No sequence matches with given settings" unless $seq_count > 0;
printf "%6.2f\t%d\t%d\t%s\t%d\t%s%s\n",
$clade_counts{0} * 100 / $seq_count,
$clade_counts{0}, $taxo_counts{0}, "U",
0, "", "unclassified";
dfs_report(1, 0);
sub dfs_report {
my $node = shift;
my $depth = shift;
if (! $clade_counts{$node} && ! $show_zeros) {
return;
}
printf "%6.2f\t%d\t%d\t%s\t%d\t%s%s\n",
($clade_counts{$node} || 0) * 100 / $seq_count,
($clade_counts{$node} || 0),
($taxo_counts{$node} || 0),
rank_code($rank_map{$node}),
$node,
" " x $depth,
$name_map{$node};
my $children = $child_lists{$node};
if ($children) {
my @sorted_children = sort { $clade_counts{$b} <=> $clade_counts{$a} } @$children;
for my $child (@sorted_children) {
dfs_report($child, $depth + 1);
}
}
}
sub rank_code {
my $rank = shift;
for ($rank) {
$_ eq "species" and return "S";
$_ eq "genus" and return "G";
$_ eq "family" and return "F";
$_ eq "order" and return "O";
$_ eq "class" and return "C";
$_ eq "phylum" and return "P";
$_ eq "kingdom" and return "K";
$_ eq "superkingdom" and return "D";
}
return "-";
}
sub dfs_summation {
my $node = shift;
my $children = $child_lists{$node};
if ($children) {
for my $child (@$children) {
dfs_summation($child);
$clade_counts{$node} += ($clade_counts{$child} || 0);
}
}
}
sub load_taxonomy {
print STDERR "Loading names file ...\n";
open NAMES, "-|", "$CWD/centrifuge-inspect --name-table $centrifuge_index"
or die "$PROG: can't open names file: $!\n";
while (<NAMES>) {
chomp;
s/\t\|$//;
my @fields = split /\t/;
my ($node_id, $name) = @fields[0,1];
$name_map{$node_id} = $name;
}
close NAMES;
print STDERR "Loading nodes file ...\n";
open NODES, "-|", "$CWD/centrifuge-inspect --taxonomy-tree $centrifuge_index"
or die "$PROG: can't open nodes file: $!\n";
while (<NODES>) {
chomp;
my @fields = split /\t\|\t/;
my ($node_id, $parent_id, $rank) = @fields[0,1,2];
if ($node_id == 1) {
$parent_id = 0;
}
$child_lists{$parent_id} ||= [];
push @{ $child_lists{$parent_id} }, $node_id;
$rank_map{$node_id} = $rank;
}
close NODES;
}
|
