kraken_summary_reports_to_species_table.pl

#!/usr/bin/env perl

# Converts Kraken summary reports to table of species found in samples.

# Kraken summary report has columns (as described in
# https://ccb.jhu.edu/software/kraken/MANUAL.html#output-format):
# - score (?)
# - total reads in the taxon, including children
# - reads assigned to this taxon specifically
# - rank (S for species)
# - taxon id
# - taxon name

# Output table has columns:
# - file path of kraken summary report
# - species taxon id
# - species name
# - total reads assigned to taxon, including children


# Usage:
# perl kraken_summary_reports_to_species_table.pl [list of kraken summary reports]

# Prints to console. To print to file, use
# perl kraken_summary_reports_to_species_table.pl [list of kraken summary reports]
# > [output table file path]


use strict;
use warnings;


my $kraken_summary_reports = $ARGV[0];


my $READS_IN_TAXON_COLUMN = 1;
my $RANK_COLUMN = 3;
my $TAXON_ID_COLUMN = 4;
my $TAXON_NAME_COLUMN = 5;

my $SPECIES_RANK = "S";

my $NEWLINE = "\n";
my $DELIMITER = "\t";


# verifies that kraken summary report exists and is non-empty
if(!$kraken_summary_reports or !-e $kraken_summary_reports or -z $kraken_summary_reports)
{
	print STDERR "Error: input kraken summary report file not provided, does not exist, "
		."or is empty:\n\t".$kraken_summary_reports."\nExiting.\n";
	die;
}


# prints header line
print "sample".$DELIMITER;
print "species_taxon_id".$DELIMITER;
print "species_name".$DELIMITER;
print "number_reads".$NEWLINE;


# reads in kraken summary reports, one by one
open KRAKEN_SUMMARY_REPORTS, "<$kraken_summary_reports"
	|| die "Could not open $kraken_summary_reports to read; terminating =(\n";
while(<KRAKEN_SUMMARY_REPORTS>) # for each line in the file
{
	chomp;
	if($_ =~ /\S/) # non-empty line
	{
		my $kraken_summary_report = $_;
	
		# reads in kraken summary report
		open KRAKEN_SUMMARY_REPORT, "<$kraken_summary_report"
			|| die "Could not open $kraken_summary_report to read; terminating =(\n";
		while(<KRAKEN_SUMMARY_REPORT>) # for each line in the file
		{
			chomp;
			my $line = $_;
			if($line =~ /\S/) # non-empty line
			{
				my @items = split($DELIMITER, $line);
				my $reads_in_taxon = $items[$READS_IN_TAXON_COLUMN];
				my $rank = $items[$RANK_COLUMN];
				my $taxon_id = $items[$TAXON_ID_COLUMN];
				my $taxon_name = $items[$TAXON_NAME_COLUMN];
				
				if(defined $rank and $rank eq $SPECIES_RANK)
				{
					if($taxon_name =~ /^\s*(\S.*\S)\s*$/)
					{
						$taxon_name = $1;
					}
				
					print $kraken_summary_report.$DELIMITER;
					print $taxon_id.$DELIMITER;
					print $taxon_name.$DELIMITER;
					print $reads_in_taxon.$NEWLINE;
				}
			}
		}
		close KRAKEN_SUMMARY_REPORT;
	}
}
close KRAKEN_SUMMARY_REPORTS;


# June 9, 2023
# December 10, 2024