Shell Programming and Scripting

awk '
        BEGIN {
                print "Algorithm\tPrediction\tLower ragne"
        }
        function checkIDX(a)
        {
                n = split ( I[a], T, "," )
                for ( i = 1; i <= n; i++ )
                {
                        if ( T[i] == $1 )
                                F = 1
                }
                return F
        }
        NR > 1 {
                F = 0
                if ( $2 in A )
                {
                        split ( A[$2], R )
                        if ( $3 >= R[2] && $4 <= R[3] )
                        {
                                L[$2]++
                                if ( checkIDX($2) != 1 )
                                        I[$2] = I[$2] OFS $1
                        }
                        if ( $3 <= R[2] && $4 >= R[3] )
                        {
                                L[$2]++
                                if ( checkIDX($2) != 1 )
                                        I[$2] = I[$2] OFS $1
                                A[$2] = $2 "\t" $3 "\t" $4
                        }
                        if ( ( $3 > R[3] ) || ( $4 < R[2] ) )
                        {
                                print I[$2] "\t" A[$2] "\t" L[$2]
                                A[$2] = $2 "\t" $3 "\t" $4
                                L[$2] = 1
                                I[$2] = $1
                        }
                }
                if ( ! ( $2 in A ) )
                {
                        A[$2] = $2 "\t" $3 "\t" $4
                        L[$2]++
                        I[$2] = $1
                }
        }
        END {
                for ( k in I )
                {
                        print I[k] "\t" A[k] "\t" L[k]
                }
        }
' OFS=, file

Algorithm       prediction
A       x       65      85
B       x       70      80
C       x       75      85
D       x       10      20
B       y       125     130
C       y       120     140
D       y       200     210

Algorithm       Prediction      Lower ragne
A,B,C   x       65      85      3
B,C     y       120     140     2
D       x       10      20      1
D       y       200     210     1

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

open my $input, "<", "$ARGV[0]" or die "cannot open file: $ARGV[0]";

my %ranges;
while (my $line = <$input>) {
  next if $. == 1;
  chomp $line;
  my ($alg, $pred, $lower, $upper) = split /[ \t]+/, $line;
  my $range = (grep {$lower>=(split /:/, $_)[0] && $lower<=(split /:/, $_)[1]} keys %ranges)[0];
  if ( !$range ) {
    push @{$ranges{"$lower:$upper"}{algs}}, $alg;
    $ranges{"$lower:$upper"}{pred} = $pred;
    search_and_include($lower, $upper, \%ranges);
  } else {
    push @{$ranges{$range}{algs}}, $alg;
    $ranges{$range}{pred} = $pred;
  }
}

foreach my $range (keys %ranges) {
  print "Algorithm\tpredicted_gene\tstart_point\tend_point\tNumber_of_algorithms_predicting_this_site\n";
  my $algs = join ", ", @{$ranges{$range}{algs}};
  my $algs_count = scalar @{$ranges{$range}{algs}};
  my ($lower, $upper) = split /:/, $range;
  print join "\t", $algs, $ranges{$range}{pred}, $lower, $upper, $algs_count;
  print "\n";
}

sub search_and_include {
  my ($lower_inc, $upper_inc, $ranges) = @_;
  foreach my $range (keys %ranges) {
    my ($lower, $upper) = split /:/, $range;
    if ($lower >= $lower_inc && $upper <= $upper_inc && ($lower ne $lower_inc || $upper ne $upper_inc)) {
      push @{$ranges{"$lower_inc:$upper_inc"}{algs}}, @{$ranges{$range}{algs}};
      delete $ranges{$range};
    }
  }
}

./script.pl file