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Re^3: Creating 2 arrays from a larger array

by tangent (Curate)
on Mar 08, 2012 at 03:32 UTC ( #958419=note: print w/ replies, xml ) Need Help??


in reply to Re^2: Creating 2 arrays from a larger array
in thread Creating 2 arrays from a larger array

You are in a loop, so $dnaString is being added to everytime the line doesn't match your start pattern. $dnaString is always one step behind @seqList so when you come to the next start line, it pushes the previous $dnaString onto @sequences, then clears it for the next iteration. Best thing to do is try it: set $count = 1 and see what happens.

Update: after re-reading this I'm a bit confused myself. Better to put a print statement within the loop:

my $dnaString = ''; ... if ($line=~/^>(\S+)/){ print qq|Count: $count, Match: $1, String: $dnaString\n|; push (@seqList, $1);


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Re^4: Creating 2 arrays from a larger array
by imtakinbioinformatic (Initiate) on Mar 08, 2012 at 04:08 UTC
    uggg still not getting it. No errors but the elements I printed were all the same. I'll keep working, thanks for explaining!
      A HASH makes more sense for this structure:
      my ($k,$v, %seq); for my $line (<DATA>) { chomp ($line); if ( $line=~/^>(\S+)\s*(.*)/){ $k=$1; $v=$2; }else{ $v=$line; } $seq{$k} .= $v; } #---- Print it ---- for my $k(sort keys %seq){ print "$k \t=> $seq{$k}\n"; } # --- Output ---(Using the __DATA__ block above) ..- # 123 => blahabcdefghijkl # 456 => de dahmnopqr # 789 => nothing wanted herestuvwxyz

                   All great truths begin as blasphemies.
                         ― George Bernard Shaw, writer, Nobel laureate (1856-1950)

      but the elements I printed were all the same
      Can you post some sample data?
      Oh it works! It seemed important that the variables were my variables? Thank you soooo much!!
Re^4: Creating 2 arrays from a larger array
by imtakinbioinformatic (Initiate) on Mar 08, 2012 at 14:52 UTC
    Yeah here's the file http://www.med.nyu.edu/rcr/rcr/course/smutans.fas

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