[boetsie]

Here you go. You had a mistake in your code, you took the third column as your contig in this line;

my $contig = $s[2];

while the contig was in the second column.

In addition, since you only have a subset of your data, you'll get these warnings. I removed the use warnings line. Run the script as;

perl script.pl Sample_aligned_reads.txt sample_contig.txt

#!usr/bin/perl-w
use strict;

open(SAM,$ARGV[0]);
my %hash = ();
while(<SAM>){
  chomp;
  next if($_ =~ /^@/); ## remove the headers in sam file
  #split the line and obtain the read and contig
  my ($read,$contig,$sequence) =split;
#split the read on the '|' character, to obtain the weight
  my (undef, $weight) = split(/\|/,$read);
#save the total number of reads and clusters in the hash
  $hash{$contig}{'clusters'}++;
  $hash{$contig}{'total'}+=$weight;
}
close SAM;


open(CTG,$ARGV[1]);
my ($contigSeq,$prevhead) = ("","");
while(<CTG>){
  chomp;
  $contigSeq.= $_ if(eof(CTG));
  if (/\>(\S+)/ || eof(CTG)){
     my $head=$1;
     if($contigSeq ne ''){
       #$contigSeq is the contig sequence, $prevhead is your contig
       my $len = length($contigSeq);
       #Now print the results
       print "$prevhead\t$len\t$hash{$prevhead}{'clusters'}\t$hash{$prevhead}{'total'}\t$contigSeq\n" if(defined $hash{$prevhead});
     }
     $prevhead = $head;
     $contigSeq='';
  }else{
     $contigSeq .= $_;
  }
}
close CTG;

[bambus]

Yes,I am sorry forgot to mention , I modified the data while extracting the columns of interest from original SAM file,but now I executed the script on complete data files.

Again I will try with this modified script.

[bambus]

Oh great! its working,thank you very much.

[boetsie]

Great, good luck with your analysis.

[bambus]

Thank you once again.