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Top Forums Shell Programming and Scripting Rewrite sed to perl or run sed in perl Post 302940843 by cmccabe on Thursday 9th of April 2015 11:58:34 AM
Old 04-09-2015
Almost perfect... the last 3 fields in the attached output 13 20763121 20763121 , I believe come from the while clause, is there a way to remove those fields? Thank you for your help Smilie.

Code:
parse() {
    printf "\n\n"
	cd 'C:\Users\cmccabe\Desktop\annovar'
    perl -ne 'next if $. == 1;
	if(/.*del([A-Z]+)ins([A-Z]+).*NC_0{4}([0-9]+).*g\.([0-9]+)_([0-9]+)/)   # indel
{
        print join("\t", $3, $4, $5, $1, $2), "\n";
}
            while (/\t*NC_(\d+)\.\S+g\.(\d+)(\S+)/g) {                                            # conditional parse
                ($num1, $num2, $common) = ($1, $2, $3);
                $num3 = $num2;
                if    ($common =~ /^([A-Z])>([A-Z])$/)   { ($ch1, $ch2) = ($1, $2) }              # SNP
                elsif ($common =~ /^del([A-Z])$/)        { ($ch1, $ch2) = ($1, "-") }             # deletion
                elsif ($common =~ /^ins([A-Z])$/)        { ($ch1, $ch2) = ("-", $1) }             # insertion
                elsif ($common =~ /^_(\d+)del([A-Z]+)$/) { ($num3, $ch1, $ch2) = ($1, $2, "-") }  # multi deletion
				elsif ($common =~ /^_(\d+)ins([A-Z]+)$/) { ($num3, $ch1, $ch2) = ("-", $1, $2) }  # multi insertion
                printf ("%d\t%d\t%d\t%s\t%s\n", $num1, $num2, $num3, $ch1, $ch2);                 # output
                map {undef} ($num1, $num2, $num3, $common, $ch1, $ch2);
            }
           ' C:/Users/cmccabe/Desktop/annovar/out_position.txt > C:/Users/cmccabe/Desktop/annovar/out_parse.txt
		   annovar
}

 

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CURL_MULTI_ADD_HANDLE(3)						 1						  CURL_MULTI_ADD_HANDLE(3)

curl_multi_add_handle - Add a normal cURL handle to a cURL multi handle

SYNOPSIS
int curl_multi_add_handle (resource $mh, resource $ch) DESCRIPTION
Adds the $ch handle to the multi handle $mh PARAMETERS
o $mh -A cURL multi handle returned by curl_multi_init(3). o $ch -A cURL handle returned by curl_init(3). RETURN VALUES
Returns 0 on success, or one of the CURLM_XXX errors code. EXAMPLES
Example #1 curl_multi_add_handle(3) example This example will create two cURL handles, add them to a multi handle, and process them asynchronously. <?php // create both cURL resources $ch1 = curl_init(); $ch2 = curl_init(); // set URL and other appropriate options curl_setopt($ch1, CURLOPT_URL, "http://www.example.com/"); curl_setopt($ch1, CURLOPT_HEADER, 0); curl_setopt($ch2, CURLOPT_URL, "http://www.php.net/"); curl_setopt($ch2, CURLOPT_HEADER, 0); //create the multiple cURL handle $mh = curl_multi_init(); //add the two handles curl_multi_add_handle($mh,$ch1); curl_multi_add_handle($mh,$ch2); $running=null; //execute the handles do { curl_multi_exec($mh,$running); } while($running > 0); //close all the handles curl_multi_remove_handle($mh, $ch1); curl_multi_remove_handle($mh, $ch2); curl_multi_close($mh); ?> SEE ALSO
curl_multi_remove_handle(3), curl_multi_init(3), curl_init(3). PHP Documentation Group CURL_MULTI_ADD_HANDLE(3)
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