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Re^2: fasta hash

by morio56 (Initiate)
on Aug 26, 2011 at 13:51 UTC ( #922613=note: print w/replies, xml ) Need Help??

in reply to Re: fasta hash
in thread fasta hash

Thanks. But then what will be the value to the id key since te ids file only contain ids and nothing else?

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Re^3: fasta hash
by ForgotPasswordAgain (Deacon) on Aug 26, 2011 at 22:37 UTC

    As moritz said, 1 (or ++) is a common choice of value, but it's not necessarily the best one. It doesn't usually matter these days for 100k elements, but it's better (thanks, Liz! ;) for memory size to do something like this:

    my ($undef); while (whatever...) { .... $hash{$key} = $undef; }

    This way each element points to the same $undef value. Otherwise, each element would point to a different copy of the value 1. That's a kind of "poor man's aliasing". For bonus points, you might look at Array::RefElem or Data::Alias.

Re^3: fasta hash
by moritz (Cardinal) on Aug 26, 2011 at 13:56 UTC

      I have changed the code, but now my problem seems to be that I can only access the last line of the output outside the loops. I wonder if there's a way to store the variables inside the loop to be accessible outside. The code looks like this now.

      if(@ARGV < 3){ die "Not enough arguments\n"; } $sequence=""; $fastaID; open(FILE1,"$ARGV[0]") or die "No fasta file provided in command line: + $!\n"; while ($line=<FILE1>){ chomp($line); if ($line=~/^\s*$/){ next; }elsif ($line=~/^.*$/){ $fastaID=$line; $fastahash{$fastaID}=1; } } open(FILE2,"$ARGV[2]") or die "No fasta file provided in command line: + $!\n"; while($line2=<FILE2>){ chomp($line2); if ($line2=~/^>/){ @data=split(" ",$line2); $fasta=$data[1]; $sequence=""; }else{ $sequence.=$line2; } } if (exists $fastahash{$fasta}){ print "$fastaID\t $sequence\n"; } exit;

      And the output, which is just the last key value in the fastahash is

      2056360013 Musacgagchagshgashcgahcgacacsasasasacsacsasasacacaasc +assacsaascascascascac

        Sadly you ignored half of my advice; it wasn't given without reason. Please reconsider your position.

        You print can only be executed once because it's not inside a loop (should be inside the while loop). Proper indention would have made that obvious, and use strict would have told you that $fasta isn't in scope in the if (exists $fastahash{$fasta}) (if you would have declared it properly inside the while loop).

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