Re^2: Use of uninitialized value in string eq

Hi ikegami, thanks for the reply.

I do not see why there would be a problem with the assignment of one value to @temp. My intention was to put the protein sequence (of human gi) into an array and then to point a position in this sequence. I thought I would bump into the problem you mentioned in case I would have used $temp, and actually that's why I used an array there. I would be glad if you can tell me what might be the problem.

Suspicious, indeed. Yet it is working properly. I first used (\w)(\d+)(\w) and then modified it as to have the current one following the errors I got. I guess it first makes a split as P and 82L and then makes a second split by separating 82 and L. Your alternative looks more appropriate to use though.

Any idea concerning the use of 'eq' operator?

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Re^3: Use of uninitialized value in string eq by johngg (Canon) on Apr 21, 2010 at 22:42 UTC
Any idea concerning the use of 'eq' operator? ikegami has already given you the answer to that. Your line `my @temp = $info{$humangi};` [download] assigns a single scalar value to element zero only of the `@temp` array and no other element is initialised, but your line `my ($source, $position, $sink) = split(/(\d+)(\w)/, $Variant);` [download] assigns the value of 82 to `$position` using your example of "P82L" in `$Variant`. Your comparison `if ( $temp[$position] eq $source) {` [download] attempts to access element 82 of `@temp` which does not exist, hence the warning. I hope this clarifies things for you. Cheers, JohnGG	[reply] [d/l] [select]
Re^3: Use of uninitialized value in string eq by ikegami (Patriarch) on Apr 21, 2010 at 22:33 UTC
I do not see why there would be a problem with the assignment of one value to @temp. What do you think `$temp[82]` returns when `@temp` only has one value? `undef`. I guess it first makes a split as P and 82L `split` is designed to split a separated list, but there's no separator between the fields in "P82L". Yet it is working properly. In the same sense that towing your car to work is a working alternative to driving to work.	[reply] [d/l] [select]
Re^4: Use of uninitialized value in string eq by sophix (Sexton) on Apr 22, 2010 at 02:06 UTC
Thank you John and ikegami. As I was afraid, it seems that I do still have difficulties with the basics of Perl (or rather of programming). So the problem seems to have started when I first read the sequence line as `$info{$gi}=$line;`. And then, `@temp = $info{$humangi}` operates as such `$temp[0] = $info{$humangi}`. I hope I get this right. Thus, a possible solution is to store the sequence into an array in the beginning. To be frank, I do not know how to do this. Alternatively, there might be a way to convert a scalar value to an array list. (I would use `split` but as I see from your last comment on the use of split function, this is not a good way to do it. Can you help me on this one?	[reply] [d/l] [select]
Re^5: Use of uninitialized value in string eq by chromatic (Archbishop) on Apr 22, 2010 at 07:40 UTC
Thus, a possible solution is to store the sequence into an array in the beginning. To be frank, I do not know how to do this. If you show us some lines of data and explain how to identify individual components in a sequence (such that we know which is the 82nd, for example), we can explain how to write that code.	[reply]
Re^6: Use of uninitialized value in string eq by sophix (Sexton) on Apr 22, 2010 at 23:41 UTC
Re^5: Use of uninitialized value in string eq by ikegami (Patriarch) on Apr 22, 2010 at 17:06 UTC
I did not present a solution because it's not clear what you are trying to do. Giving us input samples and the output you expect to get from those inputs would be useful.	[reply]