Setting Conditional Variable Based on Partial Match

Osiris1975 has asked for the wisdom of the Perl Monks concerning the following question:

Greetings monks. I am having difficulties with the following code, in which I am trying to conditionally assign a variable based on matching the first character of a string contained in 2 other variables.

     if ($B1=~ m/^*/ | $B2=~ m/^*/) {
       my $type;
       $type eq "S";
     } else {
       $type eq "I";
     }
[download]

Basically, I am searching two other variables, if either of them have "*" as the first character, then variable $type should be set to the character variable S, otherwise it should be set to I. The error message I am getting is: Global symbol "$type" requires explicit package name at /home/radon00/amr/sandbox/alpha/SNPtagger.pl line 48. Global symbol "$type" requires explicit package name at /home/radon00/amr/sandbox/alpha/SNPtagger.pl line 51. So I think the problem has to do with the fact that I am using the $type variable which is declared in the if block, and the $B1 and $B2 variables which were declared outside of the if block. I'm just not sure what the solution is. Here is the entire code just in case some context is needed:

my $SNP_FILE="SNP.test.out"; # Will be $out in future, just hardcoded 
+to SNP.report for testing now.


open (LINES,"<$SNP_FILE") || die ("Could not open file! \n"); # Read S
+NP File
<LINES>;

while ($SNP_FILE=<LINES>) 
  {
    
     my ($contig, $PP, $UPP, $Cons, $Cov, $Conflicts, $B1, $B2)=split(
+'\t', $SNP_FILE); #Split line of SNP File
     my $ratio=sprintf("%.2f",($Conflicts/$Cov)); #Creates new variabl
+e of ratio of Conflict Count/Total Coverage

     $PP=$PP+1; # Bump padded position coordinate by 1, as gap4 coordi
+nates are off by 1 base compared to bank file
     $Cons=~ s/-/*/; # Replace - with gap4 pad notation in consensus v
+ariable
     $B1=~ s/-/*/;   # Replace - with gap4 pad notation in Base 1 vari
+able
     $B2=~ s/-/*/;   # Replace - with gap4 pad notation in Base 2 vari
+able
     chomp $B2;
     $contig=~ s/Contig/#/; # Replace contig with number sign so gap4 
+can recognize contig identifier
     if ($B1=~ m/^"*"/ or $B2=~ m/^"*"/) {
       my $type eq "S";
     } else {
       my $type eq "I";
     }
my $type;
     print "$contig $PP $Cons $Cov $Conflicts $B1 $B2 $ratio $type \n"
+;
 }
close (LINES);
[download]

Thanks for the help in advance!

Comment on Setting Conditional Variable Based on Partial Match Select or Download Code

Replies are listed 'Best First'.
Re: Setting Conditional Variable Based on Partial Match by ikegami (Patriarch) on Dec 19, 2008 at 19:40 UTC
I think the problem has to do with the fact that I am using the $type variable which is declared in the if block, and the $B1 and $B2 variables which were declared outside of the if block. Half-right. The problem is that $type is declared in the if block, but it's used outside of the block. `my $type; if ($B1=~ /^\/ \|\| $B2=~ /^\/) { $type = "S"; } else { $type = "I"; }` [download] or `my $type = $B1 =~ /^\/ \|\| $B2 =~ /^\/ ? "S" : "I";` [download] or `my $type = grep(/^\/, $B1, $B2) ? "S" : "I";` [download] You're confusing `eq` (string comparison) for `=` (assignment). See perlop `\|` is for bit math. You want `\|\|`. See perlop "``" is a special character in regexp patterns. You want "`\*`" to match that character. See perlre I didn't read any further. Hopefully, that will give you a good start.	[reply] [d/l] [select]
Re: Setting Conditional Variable Based on Partial Match by ccn (Vicar) on Dec 19, 2008 at 19:41 UTC
First of all: use `use strict;` and `use warnings;`. That will save a lot of time for you. It will be good to put backslash before `` in regexp if you want to match an asterisk. (see perldoc perlre about metacharacters) Yes `$type` must be declared outside of condition block. But rather before `if` clause than after it. And seems you want to use `=` instead of `eq` when assigning a value to `$type` `my $type = ($B1 =~ m/^\/ or $B2 =~ m/^\*/) ? 'S' : 'I';` [download]	[reply] [d/l] [select]
Re^2: Setting Conditional Variable Based on Partial Match by Osiris1975 (Novice) on Dec 23, 2008 at 20:43 UTC
Thanks for the response. I actually do use strict and warnings, I just left them out of the code that I pasted here. I'll include everything in my program in the future. The backslash tells perl to recognize the character "as is" and not as a special character, correct?	[reply]
Re^3: Setting Conditional Variable Based on Partial Match by ccn (Vicar) on Dec 24, 2008 at 10:20 UTC
> The backslash tells perl to recognize the character "as is" and not as a special character, correct? Yes with some exceptions: \t tab (HT, TAB) \n newline (NL) \r return (CR) \f form feed (FF) \b backspace (BS) \a alarm (bell) (BEL) \e escape (ESC) \033 octal char (example: ESC) \x1b hex char (example: ESC) \x{263a} wide hex char (example: SMILEY) \c[ control char (example: ESC) \N{name} named Unicode character \l lowercase next char \u uppercase next char \L lowercase till \E \U uppercase till \E \E end case modification \Q quote non-word characters till \E see: perldoc perlop (Quote and Quote-like Operators)	[reply]
Re: Setting Conditional Variable Based on Partial Match by Lawliet (Curate) on Dec 19, 2008 at 19:41 UTC
Are you trying to assign the value 'S' or 'I' to the variable $type? If so, use `=`, not `eq`. It is the assignment operator. Update (~2min after initial post): Ahh! Everyone just updated their replies! Mine looks pathetic now :P And you didn't even know bears could type.	[reply] [d/l] [select]
Re^2: Setting Conditional Variable Based on Partial Match by Osiris1975 (Novice) on Dec 23, 2008 at 20:41 UTC
Yes, thats what I was trying to do. Thanks for the correction :) In SAS, which I know marginally better, you use "=" for numerical assigment and "eq" for character assignments so I thought perl might be the same.	[reply]
Re: Setting Conditional Variable Based on Partial Match by toolic (Bishop) on Dec 19, 2008 at 19:42 UTC
Also, `eq` (perlop) is used for comparison, not for assignment. I think you want: `$type = "S";` [download] Side note... this: `$PP=$PP+1;` [download] can also be written more concisely as: `$PP++;` [download]	[reply] [d/l] [select]
Re: Setting Conditional Variable Based on Partial Match by Anonymous Monk on Dec 20, 2008 at 09:59 UTC
Tutorials : Variables and Scoping : Variable Scoping in Perl: the basics	[reply]