Show some code and explain where it fails and you will get help. If you don't know that already, you can and should use Text::CSV to parse the file.

My failed attempt:

my  $countref = ($t[8] =~ tr/.,//);
          my $ratioo = $countref/$t[7] ;

        if ($countref/$t[7] >0.95)  {
#       print "$t[1]\t$t[2]\t$t[3]: $ratioo \n";
       $seq .=$t[2];


        }
     elsif ($countref/$t[7] <=0.95){

         $t[8] =~ s/[.,]/$t[2]/g;

        my  $counta = ($t[8] =~ tr/aA//);
        my  $countt = ($t[8] =~ tr/tT//);
        my  $countg = ($t[8] =~ tr/gG//);
        my  $countc = ($t[8] =~ tr/cC//);

        my ($ratioa, $ratiot, $ratiog, $ratioc, $rat);
        my @rat = ();

        $ratioa = $counta/$t[7];
        $ratiot = $countt/$t[7];
        $ratiog = $countg/$t[7];
        $ratioc = $countc/$t[7];

print " $t[1] : A $ratioa T $ratiot G $ratiog C $ratioc ";
my      $rrat = \@rat;
         push (@rat, "$ratioa", "$ratiot", "$ratiog", "$ratioc");

         my $countnut = 0;
         my $i;
         my @ncode;
         my $ccode;
    for $i(0..$#rat){
        if ( $rrat->[$i]  >= 0.05){
            $i++;
          push (@ncode, $i);
         $countnut ++;
            $i--;
            }
            $ccode = join ("", @ncode);

        if ($countnut >= 3) {
#          print "N\n"; 
            $seq .= "N";
            }

#print " code:$ccode count $countnut\n"; 
     else {
     my   %hash;
       %hash = {1, 'A',
                 2,  'T',
                 3,  'G',
                 4,  'C',
                 12, 'W',
                 21, 'W',
                 13, 'R',
                 31, 'R',
                 14, 'M',
                 41, 'M',
                 23, 'K',
                 32, 'K',
                 24,  'Y',
                 42, 'Y',
            };

              print "cc", $hash{$ccode},"\n" ;

         }
  }

}
[download]

Like the other monks, I don't have a clue what your goals really are. (Try using shorter sentences when explaining things.) I took your code and data as posted, and put them together into a single file like this:

#!/usr/bin/perl

while (<DATA>) {
    next if (/^#/ or /^\s*$/);
    chomp;
    @t = split /\t/;
# your code goes here
}

__DATA__
# your data goes here
[download]

(update: I initially forgot to mention "split")

I had to edit the data to make it tab-delimited -- maybe the tabs were converted to spaces because of the way you posted it (or the way I downloaded it), but you may need to check and make sure whether your file really has the right number of tabs per line.

Anyway, your code ran and produced output with no errors. So what's the problem? If you were expecting some different sort of output, you'll need to explain how the actual output differs from the desired output.

I took the liberty of fixing the indentation in the code -- this really helps for making the code readable, and a good editor should make it easy to use proper indentation (e.g. emacs, vi, ...)

I also did some refactoring, to remove unnecessary variables, make the output more informative, and use loops where possible.

I couldn't tell what you were trying to do with your "$seq" variable... that (and the output format) is the only place where my version does something different from yours -- but I'm just guessing about what you really want.

Read more... (7 kB)

I would like to be able to help you but, as lima1 says, your description of the problem is difficult to understand. I'm afraid the code you posted in response to lima1's reply hasn't shed much light on the problem because you do not show how you are reading your file and we can only make assumptions regarding how the @t array is intialised. Also, what is the purpose of the %hash associative array (nice meaningful name, BTW :-)?

It would help us to help you if you could provide the output you would expect to get from the data you show and if you could break down your description in paras. 1 & 2 into smaller steps it might help us understand better. I find the +/- etc. malarkey particularly unclear.

Thanks a lot "graff" your inputs were quite useful. I could be able to write the code. (suggestions for the improvements are welcome) This code take the inputs: 1. raw pileup file and the 2. consensus fasta sequence(here it is named as "input.fasta"). and modifies the consensus fasta sequence based on the nucleotide frequences (if above 5%) at each position (from the read column (column 9). It also includes deletions if they above 5% in indel line (i.e. lines with * in the column 3)

>input.fasta
GATCCccagagcgttGAwgcttAgacTCCgagc
[download]

Find the complete code below: usage: perl modify.pileup.pl pileup2markedfasta input.pileup

 

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

&usage if (@ARGV < 1);

my $command = shift(@ARGV);
my %func = (pileup2markedfasta=>\&pileup2fq);

die("Unknown command \"$command\".\n") if (!defined($func{$command}));
&{$func{$command}};
exit(0);

# pileup2markedfasta 
sub pileup2fq {
  die(qq/
Usage:   modify.pileup.pl pileup2marked.fasta [options] <in.cns-pileup
+>
/) if (@ARGV == 0 && -t STDIN);

my %hash = (
   1 => 'A',
   2 => 'T',
   3 => 'G',
   4 => 'C',
   12 => 'W', 21 => 'W',
   13 => 'R', 31 => 'R',
   14 => 'M', 41 => 'M',
   23 => 'K', 32 => 'K',
   24 => 'Y', 42 => 'Y',
   34 => 'S', 43 => 'S'
);
  my $seq;

my $ConsFileName = "input.fasta" ; # Input single chromosome consensus
+ fasta file
open(INFILE, "$ConsFileName");
my $header ;
while(my $line = <INFILE>) {
   if ($line =~ m/^\>/){
       $header = $line; # Fasta header is removed; otherwise counted  
       }
   else{
     chomp $line;  # Remove the "\n"
     $seq .= $line;
}
}
close(INFILE);
print "$header";
print "$seq\n";

my @gps;
my $dsize ;
my $rseq = '';
my $report = '';
my @t;

  while (<>) {
   @t = split;
   if ($t[7] < 7){substr($seq, ($t[1]-1), 1, "N");} # minimum number (
+7) of reads 
   elsif ($t[2] eq '*') {    # checking if it is indel in the raw pile
+up
    if (($t[3] =~ /\*\/\+/)||($t[3] =~ /^\+/)){
      #print "next $t[3] \n"; 
      next;  }
    elsif ( ($t[3] =~ /\*\/\*/) && ($t[9] =~ /^\-/) && ($t[11]/$t[7] >
+=0.05) ){
          my $lenn =(length($t[9])-1);
        for (1..$lenn){ push (@gps, '-') }
        my $ndash .= '-' x ($lenn);
#       print "$t[1]: $lenn, @gps, dash** $ndash\n";
        substr($seq, $t[1], $lenn, "$ndash");
        }
      elsif ( ($t[3] =~ /\*\/\-/) && ($t[11]/$t[7] >=0.05) ){
         my $lenn =(length($t[9])-1);
        for (1..$lenn){ push (@gps, '-') }
        my $ndash .= '-' x ($lenn);
#       print "$t[1] dash*- $ndash\n";
        substr($seq, $t[1], $lenn, "$ndash");
        }
      elsif (($t[3] =~ /^\-/) && ($t[10]/$t[7] >=0.05)){
          my $lenn =(length($t[8])-1);
          for (1..$lenn){ push (@gps, '-') }
         my $ndash .= '-' x ($lenn);
#         print "$t[1] 'dash-'  $ndash\n";
          substr($seq, $t[1], $lenn, "$ndash");
         }
     }
    else {
         $dsize = scalar(@gps);
       if ($dsize >=1){shift @gps;
       #print "$dsize: $t[1]skippped\n"; 
       next; }
        else {
            my  $countref = ($t[8] =~ tr/.,//);
         if ( $countref / $t[7] > 0.95 ){next;}
         elsif ($countref/$t[7] <=0.95){

            $t[8] =~ s/[+-][0-9]+[atgcrykmswbdhvnATGCRYKMSWBDHVN]+//g;
+ # removes unwanted indels from read base lines
            $t[8] =~ s/[\@\'\&\!\^\$\*\)]+//g; # removes garbage symbo
+ls 
            $t[8] =~ s/[.,]/$t[2]/g;
            my %ratio;
            my @letters = qw/a t g c/;
            $report = " $t[1] : ";
          for my $p ( @letters ) {
          #`echo "$t[1]"`;
             my $count = eval "lc( '$t[8]' ) =~ tr/$p//";
             $ratio{$p} = $count / $t[7];
         #    print "$p: $ratio{$p}\n"; 
             $report .= sprintf( "%s %5.3f ", uc( $p ), $ratio{$p} );
             }
            my $countnut = 0;
            my @ncode =();
            for my $i (0 .. $#letters) {
            if ( $ratio{ $letters[$i] } >= 0.05 ) {
                 push @ncode, $i + 1;
                #print "$t[1], @ncode, $letters[$i]\n";
                 $countnut++;
                 }
              }
            my $ccode = join ("", @ncode);
         chomp $ccode;
         if ( ! exists( $hash{$ccode} )) {
      #     print "not $t[1], $ccode\n";
                substr($seq, ($t[1]-1), 1, "N");
              }
         else {
         #  print "yes $t[1], $ccode\n";
                substr($seq, ($t[1]-1), 1, "$hash{$ccode}");
                }
            }
        }
#     printf( "Data_line %5d : t1= %5s ; report= %s \n", $., $t[1], $r
+eport );
    }

  } # end of while
print "$header"; # printing back the fasta header
    $seq= uc($seq)  ;
#    print "$seq\n";  ;

 &p2q_post_process(\$seq) ;
#print "$header"; # printing back the fasta header
 } # end of pileup

##################

sub p2q_post_process {
   my ($seq) = @_;
   print &p2q_print_str($seq);
   }
#
sub p2q_print_str {
   my ($s) = @_;
   my $l = length($$s);
   for (my $i = 0; $i < $l; $i += 60) {
        print substr($$s, $i, 60), "\n";
       }
    }
#

sub usage {
  die(qq/
Program: modify.pileup.pl
Usage:   modify.pileup.pl <command> [<arguments>]\n
Command: pileup2markedfasta     generate maked.fasta from `pileup -c r
+aw pileup'
\n/);
}
[download]

input.pileup

2L    1    G    A    48    48    26    7    AAaaAAA    ACCCD?@
2L    2    A    A    48    0    26    7    ..,,...    AACC@BC
2L    3    T    K    18    18    26    7    .Ggg...    ACCCCCC
2L    4    C    C    57    0    37    16    .,..,,.,a.,,,,,^F,    CBCC
+BBC@3CCBBD=?
2L    5    C    C    54    0    37    17    .,..,,.,a.,,,,,,^F,    CDC
+CDACB9CCA@B?@D
2L    6    c    C    78    0    37    17    .,..,,.,,.,,,,,,,    CBCCB
+AC>9CBB@BA?A
2L    7    c    C    45    0    37    19    .,..,,.,,.+1A,,,,t,,^F,^Ft
+    CDCCDAC>;CBCBD*?DAA
2L    7    *    */*    55    0    37    19    *    A    18    1    0  
+  0    0
2L    8    a    A    162    0    21    45    ,-4gtct,-4gtct,,....,,,,,
+,.,.,,,,.,,,,,,,,...,.,.,,,,.,,,    CCCCA<;=/CCACDBCBCCCCDCCCCBBCCBDC
+CCCCDCDDCCAB
2L    8    *    */*    173    0    21    45    *    -gtct    43    3  
+  0    0    0
2L    9    g    G    87    0    37    20    .,..,,.,,.,,,,,,,,,^F,    
+CDCCCAC?BCBBCD?<DBBB
2L    10    a    A    87    0    37    20    .,..,,.,,.,,,,,,,,,,    C
+BCDABC>BCACBB:AC?4C
2L    11    g    G    90    0    37    21    .,..,,.,,.,,,,,,,,,,^F.  
+  CDCCCAC@@CDDCC<:DBABC
2L    12    c    C    117    0    14    31    ...,,*.,,-2gt.,,.,,.,...
+.......,,..    ;B6CCBBCBCACDCCCB@DCDCC8CCCABCC
2L    12    *    */-gt    21    21    14    31    *    -gt    30    1 
+   0    0    0
2L    13    g    G    90    0    37    21    .,..,,.,,.,,,,,,,,,,.    
+CDCCCAC?:CDB5?<>BB>BC
2L    14    t    T    45    0    37    6    ..,,,.-1T    CCCCCC
2L    14    *    -t/-t    56    59    37    6    -t    *    1    5    
+0    0    0
2L    15    t    T    93    0    37    22    .,..,,.,,.,,,G,,,,,,.^F. 
+   CDCDDDC<@CBB5B@ABC<ACC
2L    16    G    G    178    0    36    50    .$,$,$,$,,,,,.,,,,..,.,,
+...,,,,.,,...,....,...,,,$,,,.,    BCCCCCCCCCCCCBDBCBCCB>8CCCCBCCBDBC
+8>ACCBB6CC?CCC6C
2L    17    A    A    59    0    36    45    ,$,$,,,C,,,c..,.,,C..,,,,
+.,,...,....,..C,,,,,$.,    CCCCCBCCCBB8CACC>@;CCCCDCCCDAC-5ABCAA2CCCC
+?1A
2L    18    w    T    54    54    37    9    tTTTTttTT    CCDCCDCCC
2L    18    *    A/+A    65    279    37    9    A    *    8    1    0
+    0    0
2L    19    g    G    54    0    37    9    ....,,...    >>@@CC>BB
2L    20    c    C    57    0    37    10    ....,,...^F,    CACCCC?CB
+B
2L    21    t    T    57    0    37    10    ....,,...,    BCDCCCCCB?
2L    22    t    T    48    0    34    7    ..,.,,+4caaa,+4caaa    C?C
+CA=?
2L    22    *    */*    9    0    34    7    *    +CAAA    5    2    0
+    0    0
2L    23    A    A    48    0    34    7    .$.$,.,+1g,,    DBC?CCA
2L    23    *    */*    19    0    34    7    *    +G    6    1    0  
+  0    0
2L    24    g    G    60    0    14    33    .,...,,.-13GGCGCGCGTGCGC.
+,,A,,A,,A,..........aa..    DCBBBBDBCCCCBCCCDCBDCBCCCACCBABCC
2L    24    *    */*    61    0    14    33    *    -ggcgcgcgtgcgc    
+32    1    0    0    0
2L    25    a    A    163    0    15    49    ..$,..,,,t,.T,,,..,,,,T,
+-7attattt,,-7attattt,,,,,,....,,......,.,,..    BBCA>BCCCC:CCCC>ACCCC
+BCCCCBCCCCCCDCCCCCCCCBCBCDCC
2L    25    *    */-attattt    27    27    15    49    *    -attattt  
+  47    2    0    0    0
2L    26    c    C    32    0    0    11    ,,-4tctt,,.-4TCTT...-4TCTT
+.^!.^!,    CCC8CCCCBCA
2L    26    *    */-tctt    17    17    0    11    *    -tctt    8    
+3    0    0    0
2L    27    T    K    18    18    26    7    .Ggg...    ACCCCCC
2L    28    C    C    57    0    37    16    .,..,,.,a.,,,,,^F,    CBC
+CBBC@3CCBBD=?
2L    29    C    C    54    0    37    17    .,..,,.,a.,,,,,,^F,    CD
+CCDACB9CCA@B?@D
2L    30    g    G    87    0    37    20    .,..,,.,,.,,,,,,,,,^F,   
+ CDCCCAC?BCBBCD?<DBBB
2L    31    a    A    87    0    37    20    .,..,,.,,.,,,,,,,,,,    C
+BCDABC>BCACBB:AC?4C
2L    32    g    G    90    0    37    21    .,..,,.,,.,,,,,,,,,,^F.  
+  CDCCCAC@@CDDCC<:DBABC
2L    33    c    C    117    0    14    31    ...,,*.,,-2gt.,,.,,.,...
+.......,,..    ;B6CCBBCBCACDCCCB@DCDCC8CCCABCC
[download]

Output:

>input.fasta
GATCCccagagcgttGAwgcttAgacTCCgagc
>input.fasta
AAKMMCYA----GNTGMTGCTTARWC----AGC
[download]