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Help with key/value pairs

TheDragonReborn
Novice

Oct 19, 2008, 11:59 AM

Post #1 of 17 (2302 views)

Help with key/value pairs	Can't Post

Hello to all,

I am a newbie to Perl and am having some problems with a program that uses key/value pairs. Below is my code.

Code

## A program to take an Interactome data set and convert to unicon format for JProNet 
 
# Example input 
# YLR291C	YNL229C	CCSB-Y2H 
# YLR291C	YCR086W	CCSB-Y2H 
# YLR291C	YPR062W	CCSB-Y2H 
# YJL085W	YBR057C	CCSB-Y2H 
# YLR227C	YDR208W	CCSB-Y2H 
# YER106W	YCR086W	CCSB-Y2H 
 
# Example Output 
# 1   1   2   1 
# 2   1   3   1 
# 3   1   4   1 
# 4   5   6   1 
# 5   7   3   1 
 
 
print "Please type the file to be converted: " ; 
 
$input = <STDIN> ; 
 
chomp $input ; 
 
# Does file exist? 
unless( -e $input) 
    { 
        print "File \"$input\" does not seem to exist!!\n"; 
        exit ; 
    } 
     
# Can we open the file? 
unless( open(INPUT, $input)) 
    { 
        print "Cannot open file \"$input\"\n\n" ; 
        exit ; 
    } 
 
#counter for nodes 
$i = 1 ; 
 
#counter for output file (iteration) 
$count = 0 ; 
 
#weight value for edge 
$weight = 1 ; 
 
#array for lines (collect so that we can print after header part of fiile 
@lines ; 
 
# $endvertex is the last node iterated ( not neccessarily the last node because of multiple links) 
$endvertex = 0 ; 
 
#hash for key/value pairs between nodes ( Y12345 => 1) 
%KeyMap ; 
     
while(<INPUT>) 
    { 
        foreach $line (<INPUT>) 
            { 
                chomp($line) ; 
                @tokens = split('\s\t', $line) ; 
                   
                $node1 = $token[0] ; 
                $node2 = $token[1] ; 
                 
                # MAP THE NODES TO VALUES    
                     
                    if(exists $KeyMap{'$node1}') 
                        { 
                        } 
                    else 
                        { 
                            $KeyMap('$node1' => '$i') ; 
                             
                            # Record the highest value node (Last increment will be highest node) 
                            $endvertex = $KeyMap{'$node1'} ; 
                             
                            ++$i ; 
                        } 
                         
                    if(exists $KeyMap{'$node2'})                                
                        { 
                        } 
                    else 
                        { 
                            $KeyMap('$node2' => '$i') ; 
                             
                            # Record the highest value node (Last increment will be highest node) 
                            $endvertex = $KeyMap{'$node2'} ; 
                             
                            ++$i ; 
                        } 
 
                # Collect output lines (exp. 1   1   2   1) 
                # Print nodes in ascending order (1   1  2  1) NOT (1   2   1   1) !!! 
                if($KeyMap[$node1] < $KeyMap[$node2]) 
                    { 
                        $lines[$count] = "$count+1   $KeyMap{'$node1'}   $KeyMap{'$node2'}   $weight" ; 
                        $count = $count + 1 ; 
                    } 
                else 
                    { 
                        $lines[$count] = "$count+1   $KeyMap{'$node2'}   $KeyMap{'$node1'}   $weight" ; 
                        $count = $count + 1 ; 
                    } 
            } 
    } 
        
    # Print out header to .unicon file 
    print "Chain\n\n" ; 
     
    print "Vertexnumber= $endvertex\n" ; # The number for the last vertex will be total 
    print "Startvertex=1\n" ; 
    print "endvertex = $endvertex\n"; 
    print "vertexadd=0\n" ; 
    print "sarig=0\n\n" ; # Extra line 
     
    print "chained\n" ; 
 
    print "contact\n\n" ; # Extra line 
     
    # Print out lines   
#    foreach($row @lines) 
#       { 
#           print "$row\n" ; 
#       }              
     
    print "contactend\n\n" ;           
 
close INPUT ;

The input file would look something similar to this:

Code

YLR291C	YNL229C	CCSB-Y2H 
YLR291C	YCR086W	CCSB-Y2H 
YLR291C	YPR062W	CCSB-Y2H 
YJL085W	YBR057C	CCSB-Y2H 
YLR227C	YDR208W	CCSB-Y2H 
YER106W	YCR086W	CCSB-Y2H 
YLR010C	YDR082W	CCSB-Y2H 
YDR013W	YPR135W	CCSB-Y2H 
YLR291C	YGR267C	CCSB-Y2H 
YLR291C	YOR111W	CCSB-Y2H 
YLR291C	YLR377C	CCSB-Y2H 
YLR291C	YHR112C	CCSB-Y2H 
YLR291C	YJR057W	CCSB-Y2H 
YLR291C	YCL028W	CCSB-Y2H 
YDR439W	YCR086W	CCSB-Y2H 
YFR008W	YMR029C	CCSB-Y2H

The output should look something akin to this:

Chain

Vertexnumber= 17
Startvertex= 1
endvertex= 17
vertexadd=0
sarig=0
chainend

contact

1 1 2 1
2 1 3 1
3 1 4 1
4 5 6 1
contactend

I believe that my problem is with the way I am setting up my key/value pairs. Any suggestions would be great.

Thanks

Code

KevinR
Veteran

Oct 19, 2008, 12:31 PM

Post #2 of 17 (2299 views)

Re: [TheDragonReborn] Help with key/value pairs [In reply to]	Can't Post

Change this line:

@tokens = split('\s\t', $line) ;

change to:

@tokens = split(/\s+/, $line) ;

and retry your code
-------------------------------------------------

TheDragonReborn
Novice

Oct 19, 2008, 12:49 PM

Post #3 of 17 (2298 views)

Re: [KevinR] Help with key/value pairs [In reply to]	Can't Post

No help. My output is only printing

Chain

Vertexnumber= 1
Startvertex=1
endvertex = 0
vertexadd=0
sarig=0

chained
contact

contactend

any more suggestions?

eWish
User

Oct 19, 2008, 1:11 PM

Post #4 of 17 (2292 views)

Re: [TheDragonReborn] Help with key/value pairs [In reply to]	Can't Post

Are you using the strict pragma? If not then add this line of code to your script.

Code

use strict;

This is not correct.

Code

if(exists $KeyMap{'$node1}')

Should be:

Code

if(exists $KeyMap{$node1})

Also, this line looks wrong (which is done in more than one spot):

Code

$KeyMap('$node2' => '$i') ;

I believe that it should be more like this:

Code

$KeyMap{$node2} = $i;

(This post was edited by eWish on Oct 19, 2008, 1:19 PM)

eWish
User

Oct 19, 2008, 1:24 PM

Post #5 of 17 (2285 views)

Re: [TheDragonReborn] Help with key/value pairs [In reply to]	Can't Post

Also, I would delete the quotes around the variable $node1 and $node2.

Like so:

Code

$KeyMap{$node1}; 
$KeyMap{$node2};

By doing it the way you have it written you should be getting a literal key/value pair called $node1 and $node2 instead of the value that $node1 and $node2 hold.

KevinR
Veteran

Oct 19, 2008, 2:48 PM

Post #6 of 17 (2270 views)

Re: [TheDragonReborn] Help with key/value pairs [In reply to]	Can't Post

Maybe you understand the difference between single-quotes and double-quotes but your code does not reflect that. If not, you need to read up on single and double quoted strings and how the quotes affect variable interpolation/expansion.
-------------------------------------------------

(This post was edited by KevinR on Oct 19, 2008, 2:50 PM)

eWish
User

Oct 19, 2008, 3:52 PM

Post #7 of 17 (2265 views)

Re: [KevinR] Help with key/value pairs [In reply to]	Can't Post

I will get to reading about single and double quotes. Thanks.

KevinR
Veteran

Oct 19, 2008, 4:05 PM

Post #8 of 17 (2263 views)

Re: [eWish] Help with key/value pairs [In reply to]	Can't Post

Not you Kevin, I meant the OP. Sorry about the confusion.
-------------------------------------------------

TheDragonReborn
Novice

Oct 20, 2008, 5:27 AM

Post #9 of 17 (2253 views)

Re: [KevinR] Help with key/value pairs [In reply to]	Can't Post

Thanks for the help. However, the program still does not seem to be acting on the input file. Here is my updated code:

Code

#!/usr/bin/perl 
## A program to take an Interactome data set and convert to unicon format for JProNet 
 
use strict ; 
 
# Example input 
# YLR291C	YNL229C	CCSB-Y2H 
# YLR291C	YCR086W	CCSB-Y2H 
# YLR291C	YPR062W	CCSB-Y2H 
# YJL085W	YBR057C	CCSB-Y2H 
# YLR227C	YDR208W	CCSB-Y2H 
# YER106W	YCR086W	CCSB-Y2H 
 
# Example Output 
# 1   1   2   1 
# 2   1   3   1 
# 3   1   4   1 
# 4   5   6   1 
# 5   7   3   1 
 
 
print "Please type the file to be converted: " ; 
 
$input = <STDIN> ; 
 
chomp $input ; 
 
# Does file exist? 
unless( -e $input) 
    { 
        print "File \"$input\" does not seem to exist!!\n"; 
        exit ; 
    } 
     
# Can we open the file? 
unless( open(INPUT, $input)) 
    { 
        print "Cannot open file \"$input\"\n\n" ; 
        exit ; 
    } 
 
#counter for nodes 
$i = 1 ; 
 
#counter for output file (iteration) 
$count = 0 ; 
 
#weight value for edge 
$weight = 1 ; 
 
#array for lines (collect so that we can print after header part of fiile 
@lines ; 
 
# $endvertex is the last node iterated ( not neccessarily the last node because of multiple links) 
$endvertex = 0 ; 
 
#hash for key/value pairs between nodes ( Y12345 => 1) 
%KeyMap ; 
     
while(INPUT) 
    { 
        foreach ($line (INPUT)) 
            { 
                chomp($line) ; 
                @tokens = split(/\s+/, $line) ; 
                   
                $node1 = $tokens[0] ; 
                $node2 = $tokens[1] ; 
                 
                # MAP THE NODES TO VALUES    
                     
                    if(exists $KeyMap{$node1}) 
                        { 
                        } 
                    else 
                        { 
                            $KeyMap({$node1} = $i) ; 
                             
                            # Record the highest value node (Last increment will be highest node) 
                            $endvertex = $KeyMap{$node1} ; 
                             
                            ++$i ; 
                        } 
                         
                    if(exists $KeyMap{$node2})                                
                        { 
                        } 
                    else 
                        { 
                            $KeyMap({$node2} = $i) ; 
                             
                            # Record the highest value node (Last increment will be highest node) 
                            $endvertex = $KeyMap{$node2} ; 
                             
                            ++$i ; 
                        } 
 
                # Collect output lines (exp. 1   1   2   1) 
                # Print nodes in ascending order (1   1  2  1) NOT (1   2   1   1) !!! 
                if($KeyMap[$node1] < $KeyMap[$node2]) 
                    { 
                        $lines[$count] = "$count+1   $KeyMap{$node1}   $KeyMap{$node2}   $weight" ; 
                        $count = $count + 1 ; 
                    } 
                else 
                    { 
                        $lines[$count] = "$count+1   $KeyMap{$node2}   $KeyMap{$node1}   $weight" ; 
                        $count = $count + 1 ; 
                    } 
            } 
    } 
     
############################################################################# 
#####################   OUTPUT FOR PROGRAM ################################## 
############################################################################# 
        
    # Print out header to .unicon file 
    print "Chain\n\n" ; 
     
    print "Vertexnumber= $endvertex\n" ; # The number for the last vertex will be total 
    print "Startvertex=1\n" ; 
    print "endvertex = $endvertex\n"; 
    print "vertexadd=0\n" ; 
    print "sarig=0\n\n" ; # Extra line 
     
    print "chained\n" ; 
 
    print "contact\n\n" ; # Extra line 
     
    # Print out lines   
    foreach($row @lines) 
       { 
           print "$row\n" ; 
       }              
     
    print "contactend\n\n" ;           
 
close INPUT ;

Here is my output

Quote

Chain

Vertexnumber= 1
Startvertex=1
endvertex = 0
vertexadd=0
sarig=0

chained
contact

contactend

Any suggestions ?

KevinR
Veteran

Oct 20, 2008, 11:46 AM

Post #10 of 17 (2242 views)

Re: [TheDragonReborn] Help with key/value pairs [In reply to]	Can't Post

I still see in your program:

$KeyMap({$node1} = $i) ;

That is wrong as has been previoulsy noted, it should be:

$KeyMap{$node1} = $i;
-------------------------------------------------

TheDragonReborn
Novice

Oct 20, 2008, 11:55 AM

Post #11 of 17 (2241 views)

Re: [KevinR] Help with key/value pairs [In reply to]	Can't Post

Thanks for the reply. Sorry I missed that edit. However, still not processing the key/value pairs. I added some lines to help illustrate what I am trying to do in my new code:

Code

 
## A program to take an Interactome data set and convert to unicon format for JProNet 
 
# Example input  (Disregard the 3rd and 4th columns) 
# YLR291C	YNL229C	CCSB-Y2H 
# YLR291C	YCR086W	CCSB-Y2H 
# YLR291C	YPR062W	CCSB-Y2H 
# YJL085W	YBR057C	CCSB-Y2H 
 
 
# Example assignment of nodes to integer values 
# YLR291C => 1 
# YNL229C => 2 
# YCR086W => 3 
# YPR062W => 4 
# YJL085W => 5 
# YBR057C => 6 
 
 
# Example Output for matrix part 
 
# Counter   Node    Node    Weight  (This line will not be printed) 
#   1        1        2       1 
#   2        1        3       1 
#   3        1        4       1 
#   4        5        6       1 
 
print "Please type the file to be converted: " ; 
 
$input = <STDIN> ; 
 
chomp $input ; 
 
# Does file exist? 
unless( -e $input) 
    { 
        print "File \"$input\" does not seem to exist!!\n"; 
        exit ; 
    } 
     
# Can we open the file? 
unless( open(INPUT, $input)) 
    { 
        print "Cannot open file \"$input\"\n\n" ; 
        exit ; 
    } 
 
#counter for nodes 
$i = 1 ; 
 
#counter for output file (iteration) 
$count = 0 ; 
 
#weight value for edge 
$weight = 1 ; 
 
#array for lines (collect so that we can print after header part of fiile 
@lines ; 
 
# $endvertex is the last node iterated ( not neccessarily the last node because of multiple links) 
$endvertex = 0 ; 
 
#hash for key/value pairs between nodes ( Y12345 => 1) 
%KeyMap ; 
     
while(INPUT) 
    { 
        foreach ($line (INPUT)) 
            { 
                chomp($line) ; 
                @tokens = split(/\s+/, $line) ; 
                   
                $node1 = $tokens[0] ; 
                $node2 = $tokens[1] ; 
                 
                # MAP THE NODES TO VALUES    
                     
                    if(exists $KeyMap{$node1}) 
                        { 
                        } 
                    else 
                        { 
                            $KeyMap{$node1} = $i ; 
                             
                            # Record the highest value node (Last increment will be highest node) 
                            $endvertex = $KeyMap{$node1} ; 
                             
                            ++$i ; 
                        } 
                         
                    if(exists $KeyMap{$node2})                                
                        { 
                        } 
                    else 
                        { 
                            $KeyMap{$node2} = $i ; 
                             
                            # Record the highest value node (Last increment will be highest node) 
                            $endvertex = $KeyMap{$node2} ; 
                             
                            ++$i ; 
                        } 
                         
                # MATRIX PART !!! 
                # Collect output lines (exp. 1   1   2   1) 
                # Print nodes in ascending order (1   1  2  1) NOT (1   2   1   1) !!! 
                if($KeyMap{$node1} < $KeyMap{$node2}) 
                    { 
                        $lines[$count] = "$count+1   $KeyMap{$node1}   $KeyMap{$node2}   $weight" ; 
                        $count = $count + 1 ; 
                    } 
                else 
                    { 
                        $lines[$count] = "$count+1   $KeyMap{$node2}   $KeyMap{$node1}   $weight" ; 
                        $count = $count + 1 ; 
                    } 
            } 
    } 
     
############################################################################# 
#####################   OUTPUT FOR PROGRAM ################################## 
############################################################################# 
        
    # Print out header to .unicon file 
    print "Chain\n\n" ; 
     
    print "Vertexnumber= $endvertex\n" ; # The number for the last vertex will be total 
    print "Startvertex=1\n" ; 
    print "endvertex = $endvertex\n"; 
    print "vertexadd=0\n" ; 
    print "sarig=0\n\n" ; # Extra line 
     
    print "chained\n" ; 
 
    print "contact\n\n" ; # Extra line 
     
    # Print out lines   (Matrix part) 
    foreach($row @lines) 
       { 
           print "$row\n" ; 
       }              
     
    print "contactend\n\n" ;           
 
close INPUT ; 
 
exit ;

I am still unsure why the keys are not being assigned to values.
Any suggestions...

KevinR
Veteran

Oct 20, 2008, 12:06 PM

Post #12 of 17 (2239 views)

Re: [TheDragonReborn] Help with key/value pairs [In reply to]	Can't Post

add this line to your program:

Code

use warnings;

it will help with syntax problems, like here:

Code

while(INPUT)  
    {  
        foreach ($line (INPUT))  
         {

those four lines should be replaced with

Code

while(my $line = <INPUT>)  
    {

Fix that and retry your code.
-------------------------------------------------

(This post was edited by KevinR on Oct 20, 2008, 12:08 PM)

TheDragonReborn
Novice

Oct 23, 2008, 6:45 PM

Post #13 of 17 (2204 views)

Re: [KevinR] Help with key/value pairs [In reply to]	Can't Post

Hello to all,

Still having problems with my code.

I am trying to point a string to an integer value. This is my input file

YLR291C YNL229C CCSB-Y2H
YLR291C YCR086W CCSB-Y2H
YLR291C YPR062W CCSB-Y2H
YJL085W YBR057C CCSB-Y2H
YLR227C YDR208W CCSB-Y2H

This is the desired output

YLR291C YNL229C
1 2
YLR291C YCR086W
1 3
YLR291C YPR062W
1 4
YJL085W YBR057C
5 6
YLR227C YDR208W
7 8

I am a novice to Perl and unsure what I am doing wrong. Here is
the code

Code

$dataFile = 'test.txt' ; 
 
unless(open(DATAFILE, $dataFile))  
    { 
        print "Error !! Did not read file.\n" ; 
        exit ; 
    } 
 
$x = 1 ; 
$i = 1 ; 
 
while($line = <DATAFILE>)  
    {     
        # Test file     
        #print $line ; 
         
        @tokens = split(/\s/, $line) ;  
            
        $node1 = $tokens[0] ;  
        $node2 = $tokens[1] ;  
         
        if($KeyMap{"$node1"}) 
            { 
                return $KeyMap{$node1} ; 
            } 
        else 
            { 
                %KeyMap = ($node1 => $i) ; 
                 
                # Record the highest value node (Last increment will be highest node) 
                $endvertex = $KeyMap{$node1} ; 
                ++$i ; 
            }  
             
        if($KeyMap{"$node2"}) 
            { 
                return $KeyMap{$node2} ; 
            } 
        else 
            { 
                %KeyMap = ($node2 => $i) ; 
                 
                # Record the highest value node (Last increment will be highest node) 
                $endvertex = $KeyMap{$node2} ; 
                ++$i ; 
            } 
         
        print $node1 , "   ", $node2 ,  "\n" ;     
        print $KeyMap{$node1}, "          ", $KeyMap{$node2},"\n" ; 
        ++$x ;          
    } 
     
    close DATAFILE ; 
    print "\nendvertex = $endvertex\n" ; 
     
exit ;

Any help would be great.

KevinR
Veteran

Oct 23, 2008, 7:15 PM

Post #14 of 17 (2202 views)

Re: [TheDragonReborn] Help with key/value pairs [In reply to]	Can't Post

Whats the significance of the digits betwwen the lines?

1 2
1 3
1 4
etc
etc

How do they relate to the data?
-------------------------------------------------

KevinR
Veteran

Oct 23, 2008, 7:23 PM

Post #15 of 17 (2201 views)

Re: [TheDragonReborn] Help with key/value pairs [In reply to]	Can't Post

Fixing a couple of things in your code produces the output you desire but I don't understand what those numbers signify.

Code

$dataFile = 'test.txt' ;  
  
unless(open(DATAFILE, $dataFile))   
    {  
        print "Error !! Did not read file.\n" ;  
        exit ;  
    }  
  
$x = 1 ;  
$i = 1 ;  
  
while($line = <DATA>)   
    {      
        # Test file      
        #print $line ;  
          
        @tokens = split(/\s/, $line) ;   
             
        $node1 = $tokens[0] ;   
        $node2 = $tokens[1] ;   
          
        if($KeyMap{"$node1"})  
            {  
#                return $KeyMap{$node1} ;  
            }  
        else  
            {  
                $KeyMap{$node1} = $i;  
                  
                # Record the highest value node (Last increment will be highest node)  
                $endvertex = $KeyMap{$node1} ;  
                ++$i ;  
            }   
              
        if($KeyMap{"$node2"})  
            {  
#                return $KeyMap{$node2} ;  
            }  
        else  
            {  
                $KeyMap{$node2} = $i ;  
                  
                # Record the highest value node (Last increment will be highest node)  
                $endvertex = $KeyMap{$node2} ;  
                ++$i ;  
            }  
          
        print $node1 , "   ", $node2 ,  "\n" ;      
        print $KeyMap{$node1}, "          ", $KeyMap{$node2},"\n" ;  
        ++$x ;           
    }  
      
    close DATAFILE ;  
    print "\nendvertex = $endvertex\n" ;  
      
exit ;

Your use of the "return" function is not correct, but I am not sure what you are trying to do in those lines.
-------------------------------------------------

TheDragonReborn
Novice

Oct 24, 2008, 8:52 AM

Post #16 of 17 (2195 views)

Re: [KevinR] Help with key/value pairs [In reply to]	Can't Post

Thank you so much. Program is finally working.

KevinR
Veteran

Oct 24, 2008, 9:46 AM

Post #17 of 17 (2194 views)

Re: [TheDragonReborn] Help with key/value pairs [In reply to]	Can't Post

You're welcome.
-------------------------------------------------

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