Reg using hash of arrays in foreach loop

[natarajmtech]

Hi all,
I have defined some array variables a
*************** *************** ***********

@L=('CTT','CTC','CTA','CTG','TTA','TTG');
 
@S=('TCT','TCC','TCA','TCG','AGT','AGC');
 
@R=('CGT','CGC','CGA','CGG','AGA','AGG');
 
@V=('GTT','GTC','GTA','GTG');
 
@A=('GCT','GCC','GCA','GCG');
 
@G=('GGT','GGC','GGA','GGG');
 
@P=('CCT','CCC','CCA','CCG');
 
@T=('ACT','ACC','ACA','ACG');
 
@I=('ATT','ATC','ATA');
 
@F=('TTT','TTC');
 
@C=('TGT','TGC');
 
@Y=('TAT','TAC');
 
@Q=('CAA','CAG');
 
@N=('AAT','AAC');
 
@H=('CAT','CAC');
 
@E=('GAA','GAG');
 
@D=('GAT','GAC');
 
@K=('AAA','AAG');
 
@M=('ATG');
 
@W=('TGG');
 

*************** *************** *************** **********
and also created a hash to store the arrays in it and finally I wanted to do a foreach loop over the desired input say for example input=VEFCDAMP and to create all possible permutation of the word taken from the definition from dictionary as defined in the array.

The following is the perl script that I conceived to do the job but I am confused here how to use the forloop here to iterate through this and make permutation,
*************** *************** *************** ***************

print "\n\n\t\#################### AA 2 PROTEIN #################### \n\n";
 
print "This script will convert your amino acid sequence to DNA Sequence\n\n";
 
print "ENTER THE FILENAME OF THE Amino acid SEQUENCE:= ";
 
$aafilename = <STDIN>;
 
chomp $aafilename;
 
unless ( open(aaFILE, $aafilename) ) {
 
print "Cannot open file \"$aafilename\"\n\n";
 
}
 
@aa = <aaFILE>;
 
close aaFILE;
 
$aa = join( '', @aa);
 
print " \nThe original AA file is:\n$aa \n";
 
$aa =~ s/\s//g;
 
@aa=$aa;
 
my $protein='';
 
my $codon;
 
@L=('CTT','CTC','CTA','CTG','TTA','TTG');
 
@S=('TCT','TCC','TCA','TCG','AGT','AGC');
 
@R=('CGT','CGC','CGA','CGG','AGA','AGG');
 
@V=('GTT','GTC','GTA','GTG');
 
@A=('GCT','GCC','GCA','GCG');
 
@G=('GGT','GGC','GGA','GGG');
 
@P=('CCT','CCC','CCA','CCG');
 
@T=('ACT','ACC','ACA','ACG');
 
@I=('ATT','ATC','ATA');
 
@F=('TTT','TTC');
 
@C=('TGT','TGC');
 
@Y=('TAT','TAC');
 
@Q=('CAA','CAG');
 
@N=('AAT','AAC');
 
@H=('CAT','CAC');
 
@E=('GAA','GAG');
 
@D=('GAT','GAC');
 
@K=('AAA','AAG');
 
@M=('ATG');
 
@W=('TGG');
 
 
 
$L=\@L;
 
$S=\@S;
 
$R=\@R;
 
$V=\@V;
 
$A=\@A;
 
$G=\@G;
 
$P=\@P;
 
$T=\@T;
 
$I=\@I;
 
$F=\@F;
 
$C=\@C;
 
$Y=\@Y;
 
$Q=\@Q;
 
$N=\@N;
 
$H=\@H;
 
$E=\@E;
 
$D=\@D;
 
$K=\@K;
 
$M=\@M;
 
$W=\@W;
 
 
 
%hash = (L=>$L,S=>$S,R=>$R,V=>$V,A=>$A,G=>$G,P=>$P,T=>$T,I=>$I,F=>$F,C=>$C,Y=>$Y,Q=>$Q,N=>$N,H=>$H,E=>$E,D=>$D,K=>$K,M=>$M,W=>$W);
 
 
 
$hash_ref=\%hash;
 
 
my @aa_split = split //, $aa;
 
 
 
foreach my $val (@{hash{@aa_split}})
 
{
print "@{$val} ";
 
}
print " \n";
 

*************** *************** *************** *************** *****

to run this program please create and save a txt file with the content of word VEFCDAMP in it.

I want my program to perform simillar task what the following program does it for
*************** *************** *************** *************** ****

use strict;
use warnings;
my @V=('GTT','GTC','GTA','GTG');
my @A=('GCT','GCC','GCA','GCG');
my @E=('GAA','GAG');
my @F=('TTT','TTC');
my @G=('GGT','GGC','GGA','GGG');
my @H=('CAT','CAC');
my $i = 1;
foreach my $v (@V) {
   foreach my $a (@A) {
      foreach my $e (@E) {
         foreach my $f (@F) {
            foreach my $g (@G) {
               foreach my $h (@H) {
                  print "$i $v$a$e$f$g$h\n";
                  $i++;
               }
            }
         }
      }
   }
}
 

*************** *************** *************** *************** **

Thanks in advance,
B.Nataraj

[natarajmtech]

Hi Kevin,
Thanks once again for your help. It took some time for me to install the List::Permutor module into my system and so a delay in replying you, now your code is working fine but as you said it goes on exponential time for a larger size input. I have not much gone in detail of your code, Hope I soon understand it and will come back to you.

With Thanks,
B.Nataraj

Hi Kevin,
Sorry about my last reply, I just carried away by seeing new code and implementing new module and running the code. Infact your new code is not doing the right job, To say it short to you , I wanted the output for the word "VF" (you took this word as sample in your code) like the one come out of the following code (This is also your code) , The total permutation would be 512.

use strict;
use warnings;
my @V=('GTT','GTC','GTA','GTG');
my @A=('GCT','GCC','GCA','GCG');
my @E=('GAA','GAG');
my @F=('TTT','TTC');
my @G=('GGT','GGC','GGA','GGG');
my @H=('CAT','CAC');
my $i = 1;
foreach my $v (@V) {
   foreach my $a (@A) {
      foreach my $e (@E) {
         foreach my $f (@F) {
            foreach my $g (@G) {
               foreach my $h (@H) {
                  print "$i $v$f\n";
                  $i++;
               }
            }
         }
      }
   }
}
 
 

Hope you can now better understand the problem. In mean time I am trying to change your code the way I wanted it is to be.

Thanks for your all help,
B.Nataraj

[nithinpes]

Hi Kevin,
Sorry about my last reply, I just carried away by seeing new code and implementing new module and running the code. Infact your new code is not doing the right job, To say it short to you , I wanted the output for the word "VF" (you took this word as sample in your code) like the one come out of the following code (This is also your code) , The total permutation would be 512.
Thanks for your all help,
B.Nataraj

The total permutation for 'VF' should not be 512. It will be 8. The script you have shown will just create multiple duplicates to produce 512 results, because of usage of unnecessary foreach loops.

use strict; 
use warnings; 
my @V=('GTT','GTC','GTA','GTG'); 
my @A=('GCT','GCC','GCA','GCG'); 
my @E=('GAA','GAG'); 
my @F=('TTT','TTC'); 
my @G=('GGT','GGC','GGA','GGG'); 
my @H=('CAT','CAC'); 
my $i = 1; 
 
         foreach my $v (@V ){           
               foreach my $f (@F) { 
                  print "$i $v$f\n"; 
                  $i++; 
               } 
            } 
 
 

However, I haven't tested the output using List::Permutor. I will check it in my free-time and compare the output.

-Nithin

[natarajmtech]

The total permutation for 'VF' should not be 512. It will be 8. The script you have shown will just create multiple duplicates to produce 512 results, because of usage of unnecessary foreach loops.

use strict; 
use warnings; 
my @V=('GTT','GTC','GTA','GTG'); 
my @A=('GCT','GCC','GCA','GCG'); 
my @E=('GAA','GAG'); 
my @F=('TTT','TTC'); 
my @G=('GGT','GGC','GGA','GGG'); 
my @H=('CAT','CAC'); 
my $i = 1; 
 
         foreach my $v (@V ){           
               foreach my $f (@F) { 
                  print "$i $v$f\n"; 
                  $i++; 
               } 
            } 
 
 

However, I haven't tested the output using List::Permutor. I will check it in my free-time and compare the output.

-Nithin

Hi Nithin,

Sorry about my careless mistake and thanks for correcting it. Looking forward your next reply.

B.Nataraj

[KevinADC]

The total permutation for 'VF' should not be 512. It will be 8. The script you have shown will just create multiple duplicates to produce 512 results, because of usage of unnecessary foreach loops.

use strict; 
use warnings; 
my @V=('GTT','GTC','GTA','GTG'); 
my @A=('GCT','GCC','GCA','GCG'); 
my @E=('GAA','GAG'); 
my @F=('TTT','TTC'); 
my @G=('GGT','GGC','GGA','GGG'); 
my @H=('CAT','CAC'); 
my $i = 1; 
 
         foreach my $v (@V ){           
               foreach my $f (@F) { 
                  print "$i $v$f\n"; 
                  $i++; 
               } 
            } 
 
 

However, I haven't tested the output using List::Permutor. I will check it in my free-time and compare the output.

-Nithin

8? Then you are not talking about permutations. VF will produce 512 unique permutations with no duplicates assuming all 6 codons can be in all six positions of each permutation.

Using VF as an example, I think your requirements are:

V (first position)
F (second position)

So all the codons in @V can only ever occupy the first position of the permutations you desire. All codons in @F can only occupy the second position. There are only two positions because that is the number of letters/arrays. Using VFas the example, there can not be a permutation with TTT or TTC in the first position, for example:

TTTGTT
TTCGTT

Is that correct?

[natarajmtech]

8? Then you are not talking about permutations. VF will produce 512 unique permutations with no duplicates assuming all 6 codons can be in all six positions of each permutation.

Using VF as an example, I think your requirements are:

V (first position)
F (second position)

So all the codons in @V can only ever occupy the first position of the permutations you desire. All codons in @F can only occupy the second position. There are only two positions because that is the number of letters/arrays. Using VFas the example, there can not be a permutation with TTT or TTC in the first position, for example:

TTTGTT
TTCGTT

Is that correct?

Hi Kevin,

Exactly... yea the position should not be interchanged.

Thanks,
B.Nataraj

[nithinpes]

Hi Kevin,

Exactly... yea the position should not be interchanged.

Thanks,
B.Nataraj

List::Permutor is not the module of choice then. It will produce all possible combinations/ orders of list elements. E.g for a list with elements - 'A', 'B', 'C'.,
the possible combinations are:
A, B, C
A, C, B
B, A, C
B, C, A
C, A, B
C, B, A

But, what you are looking for is something like A can be constituted by three possible sets of codons, B by two etc.
I believe there are Bio-Perl modules which do the job that you are looking for.

[natarajmtech]

List::Permutor is not the module of choice then. It will produce all possible combinations/ orders of list elements. E.g for a list with elements - 'A', 'B', 'C'.,
the possible combinations are:
A, B, C
A, C, B
B, A, C
B, C, A
C, A, B
C, B, A

But, what you are looking for is something like A can be constituted by three possible sets of codons, B by two etc.
I believe there are Bio-Perl modules which do the job that you are looking for.

Hi Nithin,

Before coming to this forum, I tried possible code for the same in bioperl module and all possible code depository for any snippet to do my objective but my search ended in vein. Technically the approach is called "Back-translation"(bi oinformatics term). More the Bioinformatics problem that I try to address here is so unique and rare and it may not be a regular requirement for many , that’s why I suppose that this is not there to find in bioperl. that’s how I started to develop my own code and sought the help from this forum. Anyhow I would try again there then.

Thanks ,
B.Nataraj

[nithinpes]

Hi Nithin,

Before coming to this forum, I tried possible code for the same in bioperl module and all possible code depository for any snippet to do my objective but my search ended in vein. Technically the approach is called "Back-translation"(bi oinformatics term). More the Bioinformatics problem that I try to address here is so unique and rare and it may not be a regular requirement for many , that’s why I suppose that this is not there to find in bioperl. that’s how I started to develop my own code and sought the help from this forum. Anyhow I would try again there then.

Thanks ,
B.Nataraj

Here is one way of doing it. This code dynamically generates required foreach loops and executes the command.

 my $seq = 'VF'; 
my %hash = (  
   L => ['CTT','CTC','CTA','CTG','TTA','TTG'], 
   S => ['TCT','TCC','TCA','TCG','AGT','AGC'], 
   R => ['CGT','CGC','CGA','CGG','AGA','AGG'], 
   V => ['GTT','GTC','GTA','GTG'], 
   A => ['GCT','GCC','GCA','GCG'], 
   G => ['GGT','GGC','GGA','GGG'], 
   P => ['CCT','CCC','CCA','CCG'], 
   T => ['ACT','ACC','ACA','ACG'], 
   I => ['ATT','ATC','ATA'], 
   F => ['TTT','TTC'], 
   C => ['TGT','TGC'], 
   Y => ['TAT','TAC'], 
   Q => ['CAA','CAG'], 
   N => ['AAT','AAC'], 
   H => ['CAT','CAC'], 
   E => ['GAA','GAG'], 
   D => ['GAT','GAC'], 
   K => ['AAA','AAG'], 
   M => ['ATG'], 
   W => ['TGG'], 
); 
 
my @loops = split '', $seq; 
my $cmd;
local $i=0;
my $vars;
 
foreach my $letter (@loops) {
    my ($str,$v)= createloop($letter);
    $vars.=$v;
    $cmd.=$str;
} 
$cmd=$cmd.'print'. " \"$vars\\n\";";  ## adding print statement
$cmd.= '}'x$i;       ### ending statement blocks
 
eval {eval $cmd; };   ## first eval returns statement block
 
##creating foreach loops 
sub createloop {
$i++;
my $var ='$a'.$i;
return ("foreach $var (qw(@{$hash{$_[0]}})) {",$var) ;
 
}
 

[natarajmtech]

Here is one way of doing it. This code dynamically generates required foreach loops and executes the command.

 my $seq = 'VF'; 
my %hash = (  
   L => ['CTT','CTC','CTA','CTG','TTA','TTG'], 
   S => ['TCT','TCC','TCA','TCG','AGT','AGC'], 
   R => ['CGT','CGC','CGA','CGG','AGA','AGG'], 
   V => ['GTT','GTC','GTA','GTG'], 
   A => ['GCT','GCC','GCA','GCG'], 
   G => ['GGT','GGC','GGA','GGG'], 
   P => ['CCT','CCC','CCA','CCG'], 
   T => ['ACT','ACC','ACA','ACG'], 
   I => ['ATT','ATC','ATA'], 
   F => ['TTT','TTC'], 
   C => ['TGT','TGC'], 
   Y => ['TAT','TAC'], 
   Q => ['CAA','CAG'], 
   N => ['AAT','AAC'], 
   H => ['CAT','CAC'], 
   E => ['GAA','GAG'], 
   D => ['GAT','GAC'], 
   K => ['AAA','AAG'], 
   M => ['ATG'], 
   W => ['TGG'], 
); 
 
my @loops = split '', $seq; 
my $cmd;
local $i=0;
my $vars;
 
foreach my $letter (@loops) {
    my ($str,$v)= createloop($letter);
    $vars.=$v;
    $cmd.=$str;
} 
$cmd=$cmd.'print'. " \"$vars\\n\";";  ## adding print statement
$cmd.= '}'x$i;       ### ending statement blocks
 
eval {eval $cmd; };   ## first eval returns statement block
 
##creating foreach loops 
sub createloop {
$i++;
my $var ='$a'.$i;
return ("foreach $var (qw(@{$hash{$_[0]}})) {",$var) ;
 
}
 

Hi Nithin,

Thank you very much for the code, it does great and meet my objective.
I really thankful for you and Kevin for extending your kind help to me.

You guys are doing really a fantastic job.

Thanks once again,
B.Nataraj

[KevinADC]

nithinpes has posted a very interesting solution, but I urge caution using it since eval will run any code it evaluates. Just make sure you don't accidently introduce something unwise into the eval block. Its fine as its written, but read up on eval before making any changes that might have serious side effects.