I'm working on making a BED file but I'm having a problem splitting a variable to get the individual id.
Here are the data
fam_scz_uktr_eur_omni*UK1090_0_pca|PT-BHLS chr15 20301669 ...
This is my script (I escaped!)
if( $id =~ m/\|/g){
@tempID = split "\|", $id;
$id = pop(@tempID);
}
...
unless($id =~ m/FID.IID/ || $id =~ m/arrayId/ || $id =~ m/sampleId/){
$orphan{$id}=$line;
}
This is the output of the orphan hash
KEY VALUE
S fam_scz_uktr_eur_omni*UK1090_0_pca|PT-BHLS chr15 20301669 ....
It's returning the last character. What gives!?
Am I missing something here? Any help is appreciated :D
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2 answers
Just to expand a little on the answer by cts. Debug this problem by inspecting the variable @tempID.
print "@tempID\n";
Here it is when split uses double quotes:
f a m _ s c z _ u k t r _ e u r _ o m n i * U K 1 0 9 0 _ 0 _ p c a | P T - B H L S
And when you use single quotes, or the regular expression suggested by cts:
fam_scz_uktr_eur_omni*UK1090_0_pca PT-BHLS
What's happening is that when you use double-quotes, split looks for the literal string \|, not the escaped pipe. It does not find it and so returns the result "no character" which results in splitting between the characters.
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Quick question: What are you expecting out of the pop operation? If you're sure the '|' is used only once in a line, why not just take
$tempId[1]?