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Full Discussion: Perl to parse
Top Forums Shell Programming and Scripting Perl to parse Post 302939427 by cmccabe on Wednesday 25th of March 2015 11:59:48 AM
Old 03-25-2015
I have added a block of code to the script (in bold) to parse the attached file, but am getting a syntax error. Thank you Smilie.

The field to parse is NC_000013.10:g.20763145_20763146delTG

Code:
Parse rules:
1. 4 zeros after the NC_  (not always the case) and the digits before the .
2. g. ### (before underscore)  _### (# after the _)
3. TG (all letters after del)
4. -  (hyphen used in this spot)    
Desired Output: 13     20763145     20763146     TG     -

Code:
 perl -ne 'next if $. == 1;
            while (/\t*NC_(\d+)\.\S+g\.(\d+)(\S+[A-Z])/g) {     # 3 condtion parse  
                ($num1, $num2, $common) = ($1, $2, $3);
                if ($common =~ /([A-Z])>([A-Z])/) {             # SNP
                    ($ch1, $ch2) = ($1, $2)
                } elsif ($common =~ /del([A-Z])/) {             # deletion
                    ($ch1, $ch2) = ($1, "-")
				} elsif ($common =~ /ins([A-Z])/) {             # insertion
                    ($ch1, $ch2) = ("-", $1)
			while (/\t*NC_(\d+)\.\S+g\.\S+g\.(\d+)(\S+[A-Z])/g) {      # 2 condtion parse  
                ($num1, $num2, $common) = ($1, $2, $3);
                if ($common =~ /del([A-Z])/) {                        # multi deletion
                    ($ch1, $ch2) = ($1, "-")             
                } elsif ($common =~ /ins([A-Z])/) {                   # multi insertion
                    ($ch1, $ch2) = ("-", $1)
                }
                printf ("%d\t%d\t%d\t%s\t%s\n", $num1, $num2, $num2, $ch1, $ch2);    # output
                map {undef} ($num1, $num2, $common, $ch1, $ch2);
            }
           ' out_position.txt > out_parse.txt


Code:
 
syntax error at -e line 10, near ") {"
Missing right curly or square bracket at -e line 20, at end of line
syntax error at -e line 20, at EOF
Execution of -e aborted due to compilation errors.

 

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RUNKIT_METHOD_ADD(3)							 1						      RUNKIT_METHOD_ADD(3)

runkit_method_add - Dynamically adds a new method to a given class

SYNOPSIS
bool runkit_method_add (string $classname, string $methodname, string $args, string $code, [int $flags = RUNKIT_ACC_PUBLIC]) DESCRIPTION
Warning This function is EXPERIMENTAL. The behaviour of this function, its name, and surrounding documentation may change without notice in a future release of PHP. This function should be used at your own risk. PARAMETERS
o $classname - The class to which this method will be added o $methodname - The name of the method to add o $args - Comma-delimited list of arguments for the newly-created method o $code - The code to be evaluated when $methodname is called o $flags - The type of method to create, can be RUNKIT_ACC_PUBLIC, RUNKIT_ACC_PROTECTED or RUNKIT_ACC_PRIVATE Note This parameter is only used as of PHP 5, because, prior to this, all methods were public. RETURN VALUES
Returns TRUE on success or FALSE on failure. EXAMPLES
Example #1 runkit_method_add(3) example <?php class Example { function foo() { echo "foo! "; } } // create an Example object $e = new Example(); // Add a new public method runkit_method_add( 'Example', 'add', '$num1, $num2', 'return $num1 + $num2;', RUNKIT_ACC_PUBLIC ); // add 12 + 4 echo $e->add(12, 4); ?> The above example will output: 16 SEE ALSO
runkit_method_copy(3), runkit_method_redefine(3), runkit_method_remove(3), runkit_method_rename(3), runkit_function_add(3). PHP Documentation Group RUNKIT_METHOD_ADD(3)
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