surpi_blast_fastas_parse.pl

#!/usr/bin/env perl
# Read in a BLAST  file and identify the organisms at X tax level

use Bio::LITE::Taxonomy;
use Bio::LITE::Taxonomy::NCBI;
use Switch;

use warnings;

if ( $ARGV[0] eq "-h" ) { print STDERR "Usage: $0 <BLAST file dir> [ <taxlevel> <search term> ]\n\n" ; exit }

my $inputdir = $ARGV[0];
my $taxlevel = $ARGV[1] // 'superkingdom';
my $findthis = $ARGV[2] // "Virus";

opendir INDIR, $inputdir;


my @blastfiles = grep /\.blast/, readdir(INDIR);

closedir INDIR;



#my $tax = Bio::LITE::Taxonomy::NCBI->new (
#                                               names=> "/scicomp/home/fep2/taxonomy/161012/names.dmp",
#                                               nodes=>"/scicomp/home/fep2/taxonomy/161012/nodes.dmp"
#                                              );
#my $tax = Bio::LITE::Taxonomy::NCBI->new ( names=> "/tmp/taxonomy/names.dmp", nodes=>"/tmp/taxonomy/nodes.dmp" );

my $tax = Bio::LITE::Taxonomy::NCBI->new ( names=> "/scicomp/home/fep2/taxonomy/current/names.dmp", nodes=>"/scicomp/home/fep2/taxonomy/current/nodes.dmp" );

print "Sample\tTaxon\tTotal_reads\tFirstchoice\tTop10\tTopButAlone\n";

foreach my $file (@blastfiles) {
	my $lastread = "xx"; 
	my $counter = 0;	# number of reads
 	my $counter2 = 0;	# number of entries per read
	my $positive1 = 0; 	#positive for search at first result
	my $positive10 = 0;	#positive for search in other top10
	my $mark1 = 0; my $mark1a = 0; my $mark10 = 0; my $strange = 0;
	my $topeval = 1;
	open my $blastfile, "$inputdir/$file";

	my @name = split '\.',$file;
	$findthis = $name[0]; $taxlevel = 'genus'; # activate to so individual searches
	$findthis =~ s/_/ /;

	#### Exceptions based on NCBI Taxonomy changes ##
	# Find particular genera that have changed and update them to suit the newer Taxonomy download
	switch ($findthis) {
		case "Circovirus"	{ $findthis = "Gemycircularvirus" } # Apparently they changed it or something to Gemycircularvirus 2017-01-17
	}
	##################################################

	while (<$blastfile>) { 


		my @line = split '\t', $_;
#		my @taxonomy = $tax->get_taxonomy_with_levels($line[6]);
		my $levelname = $tax->get_term_at_level($line[6], $taxlevel);

		if ($lastread eq $line[0]) { 
			$counter2++;

			if ( $levelname =~ /$findthis/ ) { 
				$mark10 = 1 if $mark1 == 0;	# Mark this a read in the Top 10, if it's not already at #1
				$mark1a = 1;			# Validates the 1st place hit
			}
			
		} else { 
			$positive1++  if ( $mark1 == 1 && $mark1a == 1 );
			$positive10++ if $mark10 == 1;
			$strange++ if ( $mark1 == 1 && $mark1a == 0 );	#case where there is only one hit for that virus, and it's on top.
			$mark1 = 0; $mark10 = 0; $mark1a=0; 

			$counter2 = 1;
			$counter++;

			if ( $levelname =~ /$findthis/ ) {   # New read is what we're looking for at top of BLAST results
				#print "$line[0], $counter";
				$mark1 = 1;
#				$topeval=$line[2];	     #### TO DO - Add in Evalue check somehow to see if the first selection is much higher than the next one

			}
		}
		if (eof) {
			if ($mark1 == 1) {
				if  ( $mark1a == 1 || $counter2 == 1) { $positive1++; } 
					else { 
						$strange++; }
			}
			if ($mark10 == 1) { $positive10++ ; }
		}
		$lastread = $line[0];
	}

	print "$name[1].$name[2]\t$name[0]\t$counter\t$positive1\t$positive10\t$strange\n";
}





# Takes taxonomy array of arrays and gets the particular taxonomy
sub getTaxonByLevel  {
	my ($taxonlevel, @thistaxonomy) = @_;
	my $result = "undef";
	foreach my $i (@thistaxonomy) {
		my $z = $i->[1] ;
		if ("$z" eq "$taxonlevel") { 
			$result = $i->[0];
			last;
		}

	}
	return $result ;
}