comparison precursors.pl @ 43:4c0b1a94b882 draft

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42:3b9a6381e6bf

	}
#	print "$sarm_beg,$sarm_end $sarm\n";
#	print "$larm_beg,$larm_end $larm\n";

	# define the precursor by hybriding short arm to long arm
	my $duplex=RNA::duplexfold($sarm,$larm);
	my $struct=$duplex->{structure};
	my $energy=sprintf "%.2f", $duplex->{energy};
	my ($str1,$str2)=split(/&/,$struct);
	my $pair=$str1=~tr/(//;
#	print "pair=$pair\n";
	my $beg1=$duplex->{i}+1-length($str1);
	my $end1=$duplex->{i};
	my $beg2=$duplex->{j};
	my $end2=$duplex->{j}+length($str2)-1;
#	print "$beg1:$end1 $beg2:$end2\n";
	# transform coordinates
	$beg1=$beg1+$sarm_beg-1;
	$end1=$end1+$sarm_beg-1;
	$beg2=$beg2+$larm_beg-1;

	my $seq2=shift;
	my $like_mir_duplex=1;
	
	my $length1=length $seq1;
	my $length2=length $seq2;
	my $duplex=RNA::duplexfold($seq1, $seq2);
	my $duplex_struct=$duplex->{structure};
	my $duplex_energy=sprintf "%.2f", $duplex->{energy};
	my ($str1,$str2)=split(/&/,$duplex_struct);
	my $beg1=$duplex->{i}+1-length($str1);
	my $end1=$duplex->{i};
	my $beg2=$duplex->{j};
	my $end2=$duplex->{j}+length($str2)-1;
	
	# revise beg1, end1, beg2, end2
	$str1=~/^(\.*)/;
	$beg1+=length($1);
	$str1=~/(\.*)$/;
	$end1-=length($1);

43:4c0b1a94b882

	}
#	print "$sarm_beg,$sarm_end $sarm\n";
#	print "$larm_beg,$larm_end $larm\n";

	# define the precursor by hybriding short arm to long arm
=cut #modify in 2014-10-28
	my $duplex=RNA::duplexfold($sarm,$larm);
	my $struct=$duplex->{structure};
	my $energy=sprintf "%.2f", $duplex->{energy};
	my ($str1,$str2)=split(/&/,$struct);
	my $pair=$str1=~tr/(//;
#	print "pair=$pair\n";
	my $beg1=$duplex->{i}+1-length($str1);
	my $end1=$duplex->{i};
	my $beg2=$duplex->{j};
	my $end2=$duplex->{j}+length($str2)-1;
=cut
###### new codes begin
	my $duplex=`perl -e 'print "$sarm\n$larm"' | RNAduplex`;
	#(.(.(((.....(((.&))))))...).).   1,16  :   1,13  (-7.20)
	my @tmpduplex=split/\s+/,$duplex;
	my $struct=$tmpduplex[0];
	$tmpduplex[-1]=~s/[(|)]//g;
	my $energy=$tmpduplex[-1];
	my ($str1,$str2)=split(/&/,$struct);
	my $pair=$str1=~tr/(//;
	my ($beg1,$end1)=split/,/,$tmpduplex[1];
	my ($beg2,$end2)=split/,/,$tmpduplex[3];
######## new codes end

#	print "$beg1:$end1 $beg2:$end2\n";
	# transform coordinates
	$beg1=$beg1+$sarm_beg-1;
	$end1=$end1+$sarm_beg-1;
	$beg2=$beg2+$larm_beg-1;

	my $seq2=shift;
	my $like_mir_duplex=1;
	
	my $length1=length $seq1;
	my $length2=length $seq2;
=cut
	my $duplex=RNA::duplexfold($seq1, $seq2);
	my $duplex_struct=$duplex->{structure};
	my $duplex_energy=sprintf "%.2f", $duplex->{energy};
	my ($str1,$str2)=split(/&/,$duplex_struct);
	my $beg1=$duplex->{i}+1-length($str1);
	my $end1=$duplex->{i};
	my $beg2=$duplex->{j};
	my $end2=$duplex->{j}+length($str2)-1;
=cut
	my $duplex=`perl -e 'print "$seq1\n$seq2"' | RNAduplex`;
	#(.(.(((.....(((.&))))))...).).   1,16  :   1,13  (-7.20)
	my @tmpduplex=split/\s+/,$duplex;
	my $duplex_struct=$tmpduplex[0];
	$tmpduplex[-1]=~s/[(|)]//g;
	my $duplex_energy=$tmpduplex[-1];
	my ($str1,$str2)=split(/&/,$duplex_struct);
	#my $pair=$str1=~tr/(//;
	my ($beg1,$end1)=split/,/,$tmpduplex[1];
	my ($beg2,$end2)=split/,/,$tmpduplex[3];

	# revise beg1, end1, beg2, end2
	$str1=~/^(\.*)/;
	$beg1+=length($1);
	$str1=~/(\.*)$/;
	$end1-=length($1);