check_Blast_parsed_file.pl

#!/usr/bin/perl
use strict;
use warnings;

my $usage = "
This script will check all .blastn.parsed or .blastx.parsed files 
 to make sure parsing blast output file is finished for each file.

perl $0  <blast parsed file>
";

exit( 10 ) unless scalar @ARGV == 1;
my ( $PARSED ) = @ARGV;
my $HOME = $ENV{HOME};

my $finished = &check_blastnParsed_output($PARSED);

exit ($finished);

sub check_blastnParsed_output {
	my ( $in_file ) = @_;
	my $have_summary_line = 0;
	my $line_count = 0;
	my $total_seq = 0;
	my $saved_seq = 0;
	my $num_undefined_taxon = 0;
	
	open (TEMP, "<$in_file") or return 10;
	while (my $line = <TEMP>) {
		$line_count++;
		if ($line =~ /# Summary: (\d+) out of (\d+)/) {
			$saved_seq = $1; 
			$total_seq = $2;
			$have_summary_line = 1;
		}
		if ($line =~ /undefined taxon/) {
			$num_undefined_taxon++;
		}
	}
	close TEMP;

	if (!$have_summary_line) {
		return 10;
	}

	# taxonomy record has to be equal or greater than the number of sequences get 
	# successful phylotyped because some sequence could be assigned multiple taxonomy
	# categories. Should have at least $num_phylotyped + 1 lines
	my $num_phylotyped = $total_seq - $saved_seq;	
	if ( $num_phylotyped == 0 ) { # every sequence is unassigned
		#print "every sequence is unassigned\n";
		return 1;
	}
	# deal with situation where all records showed as undefined taxon and relative 
	# to humber of phylotyped sequences
	elsif ( $num_phylotyped <= $num_undefined_taxon) { 
		# print "every sequence is undefined taxon\n";
		return 10; #changed from 0 to 10, the system default $? is 0, avoid the same value, the same reason below
	}

	if ( ($line_count - 1) == $num_undefined_taxon) { # deal with situation where all records showed as undefined taxon
		# print "every sequence is un defined taxon\n";
		return 10;
	}

	# deal with old situation where some reads were not recorded because of no 
	# entry of gi-taxon record in the database 
	if ($num_phylotyped > ($line_count -1 ) ) {
		#print "record number less than num phylotyped\n";
		return 10;
	}

	return 1;
}