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Full Discussion: Bash code change
Top Forums Shell Programming and Scripting Bash code change Post 302945325 by cmccabe on Thursday 28th of May 2015 10:28:50 AM
Old 05-28-2015
Bash code change

I have the below bash which runs great. Before I make a change I wanted to check with experts (as I am not one). After the perl code completes, I am going to display "annotation complete" then go into the remove function .

Code:
 
annovar() {
    # combine id and position files
	cd 'C:\Users\cmccabe\Desktop\annovar'
	cp out_parse.txt "$(cat target.txt)"
	
	# run annotation
              $( perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f ")' < target.txt )
			  
     printf "The annotation is complete, would you like analyze additional target gene patients? Y/N "; read match_choice
	 case "$match_choice" in
        [yY]) id="${id}"; menu ;;
        [nN]) id="${id}"; remove ;;
		esac
}

My question is will something like this work: Thank you Smilie.

Code:
annovar() {
    # combine id and position files
	cd 'C:\Users\cmccabe\Desktop\annovar'
	cp out_parse.txt "$(cat target.txt)"
	
	# run annotation
              $( perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f ")' < target.txt )
			  
     printf "The annotation is complete "; remove
	  esac
}

 

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add element(1m) 														   add element(1m)

NAME
add element - Adds an element to a profile in a name service entry; if the specified entry does not exist, creates the entry. SYNOPSIS
rpccp add element profile-entry-name -m member {-d | -i if-id [-p priority]} [-a annotation] [-s syntax ] OPTIONS
Defines a member name for the profile element to be added (required). Performs the add element operation on the default profile element. With the -d option, the -i and -p options are ignored. Defines an interface identifier for the profile element to be added. Only one interface can be added in a single operation. An interface identifier is required, unless the default profile element is being added. With the -d option, the -i option is ignored. The value has the following form: interface-uuid,major-version.minor-version The UUID is a hexadecimal string and the version numbers are a decimal string, for example: -i ec1eeb60-5943-11c9-a309-08002b102989,3.11 Leading zeros in version numbers are ignored. Defines a search priority for the new profile element. The priority value is in the range 0 to 7, with zero having the highest priority. When a default element is added (with the -d option), the -p option is ignored. By default, a nondefault element is assigned a priority value of zero. Defines an annotation string for the profile element. Note that the shell supports quotation marks around the annotation field of profile elements, which allows you to include internal spaces in an annotation; the control program does not. To specify or refer to annotations from within the control program, limit each annotation to an unbroken alphanumeric string; for example, CalendarGroup. To refer to annotations from the system prompt, do not incorporate quota- tion marks into any annotation. Indicates the name syntax of the entry name (optional). The only value for this option is the dce name syntax, which is the default name syntax. Until an alternative name syntax becomes available, specifying the -s option is unnecessary. ARGUMENTS
Specifies the entry name of the target profile. For an entry in the local cell, you can omit the cell name and specify only the cell-rela- tive name. DESCRIPTION
The add element command adds an element to a profile in a name service entry. The name of the entry containing the profile and the entry name of the profile member in the new element are required. The entry of a profile may have been created previously (by either the add entry or add element command). But, if the specified entry does not exist, the add element command tries to create the entry. A profile element is a database record containing the following fields: This is the primary search key. The interface identifier consists of the interface UUID and the interface version numbers. The entry name of one of the following kinds of name service entries: A server entry for a server offering the requested RPC interface and object A group corresponding to the requested RPC interface A profile The pri- ority value (0 (zero) is the highest priority; 7 is the lowest) is designated by the creator of a profile element to help determine the order for using the element. NSI search operations select among like priority elements at random. For the rpccp add element command, the default is 0. The annotation string enables you to identify the purpose of the profile element. The annotation can be any textual informa- tion, for example, an interface name associated with the interface identifier or a description of a service or resource associated with a group. The annotation string is not a search key for the import or lookup operations. Privilege Required You need both read permission and write permission to the CDS object entry (the target profile entry). If the entry does not exist, you also need insert permission to the parent directory. NOTE
This command is replaced at Revision 1.1 by the dcecp command and may not be provided in future releases of DCE. EXAMPLES
The following command adds an element to the cell profile, /cell-profile, in the local cell: $ rpccp rpccp> add element > -i ec1eeb60-5943-11c9-a309-08002b102989,1.1 > -m /.:/Calendar_profile > -a RefersToCalendarGroups > /.:/cell-profile The following control program commands start the control program, set up a user profile associated with the cell profile as its default element, and add a user-specific element for the Calendar V1.1 interface, as follows: $ rpccp rpccp> add element /.:/LandS/anthro/molly_o_profile > -d -m /.:/cell-profile rpccp> rpccp> add element /.:/LandS/anthro/molly_o_profile > -m /.:/LandS/anthro/Calendar_group > -i ec1eeb60-5943-11c9-a309-08002b102989,1.1 > -a Calendar_Version 1.1_Interface rpccp> The added profile element contains the global name of the member (specified using its cell-relative name, /.:/LandS/anthro/Calendar_group) and the RPC interface identifier for the Calendar Version 1.1 interface. RELATED INFORMATION
Commands: remove element(1m), remove profile(1m), show profile(1m) add element(1m)
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