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I believe Fletch is right about the NULLs. The "concatentation" in your error message comes from interpolating the results into the string in this line:
print FILE ">$giName $gssName $definition\n$sequence";
One easy way to turn undef's into reasonable values is this idiom:
$giName ||= " ";
I don't see a lot to optimize, but here are my suggestions:
# makes array interpolate with newlines local $" = "\n"; # Pull my variable declarations outside the inner loop. my ($giName, $gssName, $definition, $sequence, @seq); while (($giName, $gssName, $definition, $sequence) = $sth2->fetchro +w_array ) { $sequence = uc( $sequence ); # If I'm right about your data, you just want to # turn the whitespace into newlines. # The following should be faster. @seq = split /\s+/,$sequence; # For any fields that can be null: $giName ||= " "; # Less interpolation will be faster, but we need it # for the array. print FILE ">",$giName," ",$gssName," ",$definition,"\n","@seq", +"\n"; }

In reply to Re: Finding error: uninitialized value in concatenation? by tall_man
in thread Finding error: uninitialized value in concatenation? by bwelch

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