--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PGAP-1.2.1/Blast_Filter.pl	Thu Jun 24 13:51:52 2021 +0000
@@ -0,0 +1,51 @@
+#!/usr/bin/perl
+use strict;
+use warnings;
+
+
+my $BLASTResult=$ARGV[0];
+my $SEQFile=$ARGV[1];
+my $coverage=$ARGV[2];
+my $identity=$ARGV[3]*100;#percents
+my $score=$ARGV[4];
+my %hash;
+my @row;
+my $line;
+
+#my $coverage=0.5;
+#my $identity=50;#percents
+#my $score=50;
+
+&ReadSeqLength("$SEQFile",\%hash);
+
+open(F,$BLASTResult);
+while ($line=<F>) 
+	{
+		if ($line!~/\#/) 
+		{
+			@row=split(/\t/,$line);
+			if ($row[2]>=$identity and $row[11]>=$score) 
+				{
+					if ((($row[7]-$row[6]+1)/$hash{$row[0]})>=$coverage) 
+						{
+							if ((($row[9]-$row[8]+1)/$hash{$row[1]})>=$coverage) 
+								{
+									print "$row[0]\t$row[1]\t$row[11]";
+								}
+						}
+				}
+		}
+	}
+close(F);
+
+sub ReadSeqLength()
+	{
+		use Bio::SeqIO;
+		(my $file,my $hash)=@_;
+		my $seq;
+		my $in=Bio::SeqIO->new(-file=>"$file",-format=>"fasta");
+		while ($seq=$in->next_seq()) 
+			{
+				$$hash{$seq->id}=length($seq->seq());
+			}
+	}
\ No newline at end of file