--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/ManipulateIntronFile.pl	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,71 @@
+#!/usr/bin/env perl
+
+use strict ;
+use warnings ;
+
+die "usage: a.pl intronA intronB [op]\n" if (@ARGV == 0 ) ;
+
+my %intronInfo ;
+my %chromRank ;
+
+sub sortIntron
+{
+	my @cols1 = split /\s+/, $a ;
+	my @cols2 = split /\s+/, $b ;
+
+	if ( $cols1[0] ne $cols2[0] )
+	{
+		$chromRank{ $cols1[0] } cmp $chromRank{ $cols2[0] } ;
+	}
+	elsif ( $cols1[1] != $cols2[1] )
+	{
+		$cols1[1] <=> $cols2[1] ;
+	}
+	else
+	{
+		$cols1[2] <=> $cols2[2] ;
+	}
+}
+
+open FP1, $ARGV[0] ;
+my $cnt = 0 ;
+while ( <FP1> )
+{
+	chomp ;
+	my $line = $_ ;
+	my @cols = split /\s+/ ;
+	push @cols, 1 ;
+	@{ $intronInfo{ $cols[0]." ".$cols[1]." ".$cols[2] } } = @cols ;
+	if ( !defined $chromRank{ $cols[0]} )
+	{
+		$chromRank{ $cols[0] } = $cnt ;
+		++$cnt ;
+	}
+}
+close FP1 ;
+
+open FP1, $ARGV[1] ;
+while ( <FP1> )
+{
+	chomp ;
+	my $line = $_ ;
+	my @cols = split /\s+/ ;
+	my $key = $cols[0]." ".$cols[1]." ".$cols[2] ;
+	next if ( !defined $intronInfo{ $key } ) ;
+	my @infoCols = @{ $intronInfo{ $key } } ;
+	$infoCols[4] = $cols[4] if ( $infoCols[4] ne "+" || $infoCols[4] ne "-" ) ;
+	$infoCols[9] |= 2  ;
+
+	@{ $intronInfo{ $key } } = @infoCols ;
+}
+close FP1 ;
+
+foreach my $key (sort sortIntron keys %intronInfo )
+{
+	my @infoCols = @{ $intronInfo{ $key } } ;
+	#print join( " ", @infoCols ), "\n" ;
+
+	next if ( $infoCols[9] != 3 ) ;
+	pop @infoCols ;
+	print join( " ", @infoCols ), "\n" ;
+}