Solved

no error but it closes on .pl run

Posted on 2007-03-17
4
165 Views
Last Modified: 2010-03-05
I need to troubleshoot the pl script below.

It takes the data entry fine until the last input, but it just close after then like below.  No error are showing.  It just closes it by itself.  What would be the cause?

thx much

To enter number N of species
5
Enter the distance (2,1)
3
Enter the distance (3,1)
2
Enter the distance (3,2)
3
Enter the distance (4,1)
4
Enter the distance (4,2)
5
Enter the distance (4,3)
3
Enter the distance (5,1)
4
Enter the distance (5,2)
5
Enter the distance (5,3)
3
Enter the distance (5,4)
3


******************************** pl script *********************************
#!/usr/bin/perl -w

# D. G. M

sub inputfile

# Dated come from a file  ($matrixfilename)

        {
        my($matfilename)=$_[0];
        my ($i,$j);
        open MAT,$matfilename or die "The file $matfilename was not found!\n";

# Determination of the number of species

        $LINE=<MAT>;
        chomp $LINE;
        @element=split / /,$LINE;
        $n=$#element+1;

   if ($n<3){
   die "To build a phylogenetic tree, minimum 3 species are needed!\n"
   }

# Initialization of the matrix of the distances

        for ($i=0;$i<=$n;$i++)
          {
          for ($j=0;$j<=$n;$j++)
             {
             $dist[$i][$j]=1000;
             }
          }

# Entry of the data

        for ($i=2;$i<=$n;$i++){
        $dist[$i][1]=$element[$i-1];
        }

        for ($j=2;$j<=$n;$j++){
        $LINE=<MAT>;
        @element=split / /,$LINE;
          for ($i=$j+1;$i<=$n;$i++){
          $dist[$i][$j]=$element[$i-1];
          }
        }
        return @dist;
}

# ---------------------------------------------------------

sub inputmatrix

# Data entered manually

{
        my ($i,$j);

        print "To enter number N of species\n";
        $n=<STDIN>;
        chop $n;

   if ($n<3){
   die "To build a phylogenetic tree, minimum 3 species are needed!\n"
   }

#  Initialization of the matrix of the distances  

        for ($i=0;$i<=$n;$i++)
          {
          for ($j=0;$j<=$n;$j++)
             {
             $dist[$i][$j]=1000;
             }
          }

# Entry of the data

        for ($i=2;$i<=$n;$i++)
          {
          for ($j=1;$j<=$i-1;$j++)
             {
             print "Enter the distance ($i,$j)\n";
             $dist[$i][$j]=<STDIN>;
             chop $dist[$i][$j];
             }
          }

# Rem: lines $i=0 et $j=0 are without utility ("neutralisee")

        return @dist;
}

# ---------------------------------------------------------

sub newmatrix
{
    my ($i,$j);
    mini(@dist);

    print "The species are grouped $q and $p ";


    for ($i=2;$i<=$n;$i++)
       {
       for ($j=1;$j<=$i-1;$j++)
           {
           if ($i==$p || $j==$p)
               {
               $dist[$i][$j]=1000;
               }
           elsif ($i!=$q && $i!=$p && $j!=$q && $j!=$p)
               {
               $dist[$i][$j]=$dist[$i][$j];
               }
           elsif ($i==$q && $j<$q)
               {
                $dist[$i][$j]=(($clu[$q])*$dist[$q][$j]+($clu[$p])*$dist[$p][$j])/($clu[$q]+$clu[$p]);
               }
           elsif ($j==$q && $i>$q && $i<$p)
               {
                $dist[$i][$j]=(($clu[$q])*$dist[$i][$q]+($clu[$p])*$dist[$p][$i])/($clu[$q]+$clu[$p]);
               }
           elsif ($j==$q && $i>$p)
               {
                $dist[$i][$j]=(($clu[$q])*$dist[$i][$q]+($clu[$p])*$dist[$i][$p])/($clu[$q]+$clu[$p]);
               }
           else
               {
               print "Bug!i=$i,j=$j,p=$p,q=$q\n";
               }
           }
       }

    $clu[$q]=$clu[$q]+$clu[$p];

    $clustr[$q]=join(",","($clustr[$q]","$clustr[$p])");
    print "\nNew Tree => $clustr[$q]  => distance=$min\n\n";

        return @dist;
}

#---------------------------------------------------------

sub mini
{

# Determination of the distance minimum

   $min=1000;
   for ($i=2;$i<=$n;$i++)
       {
       for ($j=1;$j<=$i-1;$j++)
           {
            if($min>$dist[$i][$j])
               {
               $min=$dist[$i][$j];
               $p=$i;
               $q=$j;
               }
           }
       }
    print "The distance min is $min  => ";
}

#----------------------------------------------------------

sub showmatrix

# Posting of the matrices

{
  my ($i,$j,$l);
  print "\n";

  for($l=1;$l<=$n;$l++){
  $cond[$l]=0;
  $cond[$l]=0;
  }

  $k=$k+1;

  if ($k>1){

    $kk=$k-1;
    $pp[$kk]=$p;

    for($l=1;$l<=$kk;$l++){
      for ($j=1;$j<=$n;$j++){
        if ($j==$pp[$l]){
         $cond[$j]=1;
        }
     }
    }

    for($l=1;$l<=$kk;$l++){
      for ($i=1;$i<=$n;$i++){
        if ($i==$pp[$l]){
        $cond[$i]=1;
        }
      }
    }
  }


   for ($j=1;$j<=$n;$j++){
   if ($cond[$j]==0){
      for ($i=1;$i<=$n;$i++){
      if ($cond[$i]==0){
         if ($dist[$i][$j]!=1000){
         printf "%10.2f",$dist[$i][$j];}
         else{
           print "         -";
         }
      }
      }
        print "\n";
   }
   }

        print "\n";
}

#----------------------------------------------------------

# main

my ($i);

if (scalar @ARGV==1){
   ($matrixfilename) = $ARGV[0];
   inputfile($matrixfilename);
   }
   else{
     if (scalar @ARGV==0){
     inputmatrix();
     }
     else{
     die "A number of invalid arguments!\n"
     }
   }


print "Matrix of distances in using method UPGMA.\n\n";

print "There is $n species\n\n...";

   $k=0;

# Posting of the initial matrix

   print "\n--------------------------------------------\n";
   print "Initial matrix:";
   print "\n--------------------------------------------\n";
   $p=1001;
   showmatrix (@dist);

# Initialization of the clusters & the cluster_string

for ($i=1;$i<=$n;$i++)
   {
   $clu[$i]=1;
   $clustr[$i]=$i;
   }

# Calculation and posting of the new matrices

for ($i=1;$i<=$n-1;$i++)
   {
   newmatrix(@dist);
   print "\n--------------------------------------------\n";
   print "New matrix No $i:";
   print "\n--------------------------------------------\n";
   showmatrix (@dist);
   }
0
Comment
Question by:ethanjohnsons
  • 2
4 Comments
 
LVL 84

Accepted Solution

by:
ozo earned 300 total points
ID: 18742546
When I run it, I get

To enter number N of species
5
Enter the distance (2,1)
3
Enter the distance (3,1)
2
Enter the distance (3,2)
3
Enter the distance (4,1)
4
Enter the distance (4,2)
5
Enter the distance (4,3)
3
Enter the distance (5,1)
4
Enter the distance (5,2)
5
Enter the distance (5,3)
3
Enter the distance (5,4)
3
Matrix of distances in using method UPGMA.

There is 5 species

...
--------------------------------------------
Initial matrix:
--------------------------------------------

         -      3.00      2.00      4.00      4.00
         -         -      3.00      5.00      5.00
         -         -         -      3.00      3.00
         -         -         -         -      3.00
         -         -         -         -         -

The distance min is 2  => The species are grouped 1 and 3
New Tree => (1,3)  => distance=2


--------------------------------------------
New matrix No 1:
--------------------------------------------

         -      3.00      3.50      3.50
         -         -      5.00      5.00
         -         -         -      3.00
         -         -         -         -

The distance min is 3  => The species are grouped 1 and 2
New Tree => ((1,3),2)  => distance=3


--------------------------------------------
New matrix No 2:
--------------------------------------------

         -      4.00      4.00
         -         -      3.00
         -         -         -

The distance min is 3  => The species are grouped 4 and 5
New Tree => (4,5)  => distance=3


--------------------------------------------
New matrix No 3:
--------------------------------------------

         -      4.00
         -         -

The distance min is 4  => The species are grouped 1 and 4
New Tree => (((1,3),2),(4,5))  => distance=4


--------------------------------------------
New matrix No 4:
--------------------------------------------

         -


What did you want to happen when you run it?
0
 
LVL 17

Assisted Solution

by:mjcoyne
mjcoyne earned 200 total points
ID: 18743007
I get the same output as ozo...
0
 

Author Comment

by:ethanjohnsons
ID: 18743188
that is odd..
I will try it with other inputs... again.
0
 

Author Comment

by:ethanjohnsons
ID: 18771372
yes, I got it.

thx much
0

Featured Post

Live: Real-Time Solutions, Start Here

Receive instant 1:1 support from technology experts, using our real-time conversation and whiteboard interface. Your first 5 minutes are always free.

Question has a verified solution.

If you are experiencing a similar issue, please ask a related question

Suggested Solutions

I've just discovered very important differences between Windows an Unix formats in Perl,at least 5.xx.. MOST IMPORTANT: Use Unix file format while saving Your script. otherwise it will have ^M s or smth likely weird in the EOL, Then DO NOT use m…
Email validation in proper way is  very important validation required in any web pages. This code is self explainable except that Regular Expression which I used for pattern matching. I originally published as a thread on my website : http://www…
Explain concepts important to validation of email addresses with regular expressions. Applies to most languages/tools that uses regular expressions. Consider email address RFCs: Look at HTML5 form input element (with type=email) regex pattern: T…
With Secure Portal Encryption, the recipient is sent a link to their email address directing them to the email laundry delivery page. From there, the recipient will be required to enter a user name and password to enter the page. Once the recipient …

786 members asked questions and received personalized solutions in the past 7 days.

Join the community of 500,000 technology professionals and ask your questions.

Join & Ask a Question