Gunnar,
Thanks so much for the help and the links! They help quit a bit. I decided to use the if statement you posted:
if ( $aa eq '-' ) {
$hash3{$_} .= '---';
} else {
$hash3{$_} .= substr $dna,0,3,'';
}instead of:
$hash3{$_} .= $aa eq '-' ? '---' : substr $dna,0,3,'';only because I had to add a $count++ function within the else statement (shown below) to accomplish another task within my larger script:
if ( $aa eq '-' ) {
$hash3{$_} .= '---';
} else {
$hash3{$_} .= substr $dna,0,3,'';
$count++
}I couldn't figure out if it was possible to add $count++ within the ?: statement above. I tried but could not get it to work.
However, everything works well at this point. Again, I really appreciate the help!
-Mike
On Sep 20, 2004, at 6:55 PM, [EMAIL PROTECTED] wrote:
From: Gunnar Hjalmarsson <[EMAIL PROTECTED]> Date: September 19, 2004 9:12:32 PM MDT To: [EMAIL PROTECTED] Subject: Re: Moving between hashes 2.
Michael S. Robeson II wrote:Ok, well I think I can see the forest but I have little idea as to what is actually going on here. I spent a few hours looking things up and I have a general sense of what is actually occurring but I am getting lost in the details that were posted in the last digest.
Well, before an attempt to explain and/or point you to the applicable docs, I'd like to change my mind once again. :) This is my latest idea:
my %hash3; for ( keys %hash1 ) { my $dna = $hash2{$_}; for my $aa ( split //, $hash1{$_} ) { $hash3{$_} .= $aa eq '-' ? '---' : substr $dna,0,3,''; } }
I'll assume that you don't have a problem with the outer loop, that simply iterates over the hash keys. As a first step in each iteration I copy the DNA sequence to the $dna variable, so as to not destroying %hash2.
Over to the 'tricky' part. The inner loop iterates over each character in the amino-acid sequence data, and respective character is assigned to $aa. For that I use the split() function: http://www.perldoc.com/perl5.8.4/pod/func/split.html
$hash3{$_} .= $aa eq '-' ? '---' : substr $hash2{$_},0,3,'';This is something new to me. I think I follow your use of the ?: pattern feature. However, none of the perl books I have discuss it's use in this fashion.
That sounds strange to me, because that's how it should be used... Read about the conditional operator in http://www.perldoc.com/perl5.8.4/pod/perlop.html
OTOH, that notation is basically the same as:
if ( $aa eq '-' ) { $hash3{$_} .= '---'; } else { $hash3{$_} .= substr $dna,0,3,''; }
which is a little more intuitive (at least I think it is).
So, as far as I can tell, you are saying: "hey, if you find '-' in $aa then append a '---' in $hash3, otherwise append the next three DNA letters".
Precisely.
However, I do not understand the syntax of how perl is actually doing this.
Hopefully the if/else statement makes it easier to grasp, and the '.=' operator is used just for appending something to a string.
Finally we have my use of the substr() function. http://www.perldoc.com/perl5.8.4/pod/func/substr.html It returns the first three characters in $dna, and since I also pass the null string as the fourth argument, it changes the content of $dna at the same time, i.e. it replaces the first three characters with nothing.
HTH. If you need further explanations, you'll have to ask specific questions.
-- Gunnar Hjalmarsson Email: http://www.gunnar.cc/cgi-bin/contact.pl
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