It's usually more efficient to do it the other way round: First read the file with the IDs, store the IDs in a hash, and then go through the fasta file, and print each line if its ID appears in the hash. That way you have to store less data in memory.

Regarding your code: Use strict and warnings, and indent the code properly, for example 4 characters for each opening bracket. It actually makes code readable. See perlstyle. 

@data=split(" ",$line);
$fastahash{$fastaID}=$sequence;

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This is almost certainly wrong: the hash key ($fastaID) doesn't depend on $line, so whatever it is, it's not the current ID. First assign to $fastaID, then use it as a hash key.

Perl 6 - second systems done right

In reply to Re: fasta hash by moritz
in thread fasta hash by morio56

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