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Unique entries based on a range of numbers.

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# 1  
Old 01-25-2014
Unique entries based on a range of numbers.
Hi,

I have a matrix like this:

Code:
Algorithm	predicted_gene	start_point	end_point
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

Here there are four tab-separated columns. The first column is the used algorithm for prediction, and there are 4 of them A-D. The second column are the predicted targets (which actually are genes), x and y. The third and fourth column indicate the start and the end of the predicted site in the sequence of the genes.

I'd need to unique the entries in column 2, based on the common range in the columns 3 and 4, something like this:

Code:
Algorithm	predicted_gene	start_point	end_point	Number_of_algorithms_predicting_this_site
A, B, C	x	65	85	3
D	x	10	20	1
B, C	y	120	140	2
D	y	200	210	1

Here, for example, at the first line we have algorithms A, B and C which predict the gene x, and the predicted positions all fall into the same site, i.e. the position 70-80 for algorithm B and 75-85 for algorithm C are both located inside the same predicted position by algorithm A, which is 65-85; and the last column indicates how many algorithms predicted this position. On the contrary, the predicted site by algorithm D for the entry x does not coincide with the others, so is presented in a separate line. The results for the entry y are explained in the same way.

Hope this is clear.

Thank you in advanced
Last edited by flyfisherman; 01-25-2014 at 02:42 PM..
# 2  
Old 01-25-2014
Quote:
Originally Posted by flyfisherman
Hi,

I have a matrix like this:

Code:
Algorithm	prediction	Lower ragne	Upper ragne
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

I'd need to uniq the entries in column 2 based on the number range in columns 3 and 4, plus indicating how many and which algorithms resulted the prediction, something like this:

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

Thank you in advanced

Your description is not clear to me. Please explain how do you expect above blue color highlighted result. Please explain your algorithm.
# 3  
Old 01-25-2014
Quote:
Originally Posted by Akshay Hegde
Your description is not clear to me. Please explain how do you expect above blue color highlighted result. Please explain your algorithm.
I apologize if it was not clear, I'll modify the original post.
# 4  
Old 01-25-2014
Here is an awk approach:
Code:
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

Input
Code:
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

Output
Code:
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

These 2 Users Gave Thanks to Yoda For This Post:
flyfisherman Neo
# 5  
Old 01-25-2014
Thank you Yoda for your time. Actually I edited my first post, since it was said not to be clear. In the input file I have four columns, with four headers, and in the output there is one more column, so five columns, and all are tab-delimited. Could you please modify your script based on this? Thanks
# 6  
Old 01-25-2014
Quote:
Originally Posted by flyfisherman
Thank you Yoda for your time. Actually I edited my first post, since it was said not to be clear. In the input file I have four columns, with four headers, and in the output there is one more column, so five columns, and all are tab-delimited. Could you please modify your script based on this? Thanks
Add your headers in BEGIN block edit print statement, try to learn ... after providing 99.99% of code.. if you can't edit small header information means, what I can tell. Please don't expect others to complete your task.. put little effort.
This User Gave Thanks to Akshay Hegde For This Post:
flyfisherman
# 7  
Old 01-26-2014
Perl approach:
Code:
#!/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};
    }
  }
}

Run it like this:
Code:
./script.pl file

This User Gave Thanks to bartus11 For This Post:
flyfisherman
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