comparison precursors.pl @ 46:ca05d68aca13 draft

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45:2cb6add23dfe

#Description: 
my $version=1.00;

use strict;
use Getopt::Long;
use RNA;

my %opts;
GetOptions(\%opts,"map=s","g=s","d:i","f:i","o=s","e:f","s=s","h");
if (!(defined $opts{map} and defined $opts{g} and defined $opts{o} and defined $opts{s} ) || defined $opts{h}) { #necessary arguments
&usage;
}

my $filein=$opts{'map'};
my $faout=$opts{'o'};
my $strout=$opts{'s'};
my $genome= $opts{'g'};

	}
	$tag1_end=$tag1_beg+length($tag1)-1;
	$tag2_end=$tag2_beg+length($tag2)-1;

	# fold
	my ($struct,$mfe)=RNA::fold($seq);
	$mfe=sprintf "%.2f", $mfe;
	if ($mfe > $MAX_ENERGY) {return 0;}

	# tag1
	my $tag1_length=$tag1_end-$tag1_beg+1;
	my $tag1_struct=substr($struct,$tag1_beg-1,$tag1_length);

	$seq=substr($seq,$beg-1,$end-$beg+1);
	$seq_length=length $seq;
	
	
	# fold
	my ($struct,$mfe)=RNA::fold($seq);
	$mfe=sprintf "%.2f",$mfe;
	if ($mfe > $MAX_ENERGY) {
		$pass=0;
		return $pass;
	}

46:ca05d68aca13

#Description: 
my $version=1.00;

use strict;
use Getopt::Long;
#use RNA;

my %opts;
GetOptions(\%opts,"map=s","g=s","d:i","f:i","o=s","e:f","s=s","h");
if (!(defined $opts{map} and defined $opts{g} and defined $opts{o} and defined $opts{s} ) || defined $opts{h}) { #necessary arguments
&usage;
}

my $checkno=1;
my $filein=$opts{'map'};
my $faout=$opts{'o'};
my $strout=$opts{'s'};
my $genome= $opts{'g'};

	}
	$tag1_end=$tag1_beg+length($tag1)-1;
	$tag2_end=$tag2_beg+length($tag2)-1;

	# fold
	#my ($struct,$mfe)=RNA::fold($seq);
		my $rnafold=`perl -e 'print "$seq"' | RNAfold --noPS`;
		my @rawfolds=split/\s+/,$rnafold;
		my $struct=$rawfolds[1];
		my $mfe=$rawfolds[-1];
		$mfe=~s/\(//;
		$mfe=~s/\)//;
	#$mfe=sprintf "%.2f", $mfe;
	if ($mfe > $MAX_ENERGY) {return 0;}

	# tag1
	my $tag1_length=$tag1_end-$tag1_beg+1;
	my $tag1_struct=substr($struct,$tag1_beg-1,$tag1_length);

	$seq=substr($seq,$beg-1,$end-$beg+1);
	$seq_length=length $seq;
	
	
	# fold
	#my ($struct,$mfe)=RNA::fold($seq);
		my $rnafold=`perl -e 'print "$seq"' | RNAfold --noPS`;
		my @rawfolds=split/\s+/,$rnafold;
		my $struct=$rawfolds[1];
		my $mfe=$rawfolds[-1];
		$mfe=~s/\(//;
		$mfe=~s/\)//;
	
	if ($mfe > $MAX_ENERGY) {
		$pass=0;
		return $pass;
	}