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Full Discussion: Connecting 3 files
Top Forums Shell Programming and Scripting Connecting 3 files Post 302876761 by newbie83 on Tuesday 26th of November 2013 01:03:00 PM
Old 11-26-2013
Connecting 3 files

Hi,

I`m trying to do functional categorization of a species and I need to join 3 files for that. I want to look up the code for each record in file 3 in file 1 ,
code indicated within brackets[] for example OR is the code forAt1g31340, J is the code for At1g53930.

Then I would like to find the description of the code from file 2.
The R in any code can be ignored unless it is [R] itself.
For example [OR], [JR] should be treated as [O] and [J] but [R] is treated as [R].

Actual File 1 is downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/COG/KOG/kog . I have attached a subset for testing (inline text messing up formatting)

Actual File 2 is downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/COG/KOG/fun.txt . I have attached for testing. (inline text messing up formatting)

File 3 is a list of ids to be searched
Code:
At1g53930
At2g36170

Expected output with a pipe (|) delimiter
Code:
At1g53930|O|Posttranslational modification, protein turnover, chaperones| CELLULAR PROCESSES AND SIGNALING
At2g36170|J|Translation, ribosomal structure and biogenesis| INFORMATION STORAGE AND PROCESSING

 

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globus_url_t(3) 						   globus common						   globus_url_t(3)

NAME
globus_url_t - SYNOPSIS
Data Fields char * scheme globus_url_scheme_t scheme_type char * user char * password char * host unsigned short port char * url_path char * dn char * attributes char * scope char * filter char * url_specific_part Detailed Description Parsed URLs. This structure contains the fields which were parsed from an string representation of an URL. There are no methods to access fields of this structure. Field Documentation char* globus_url_t::scheme A string containing the URL's scheme (http, ftp, etc) globus_url_scheme_t globus_url_t::scheme_type An enumerated scheme type. This is derived from the scheme string char* globus_url_t::user The username portion of the URL. [ftp, gsiftp] char* globus_url_t::password The user's password from the URL. [ftp, gsiftp] char* globus_url_t::host The host name or IP address of the URL. [ftp, gsiftp, http, https, ldap, x-nexus unsigned short globus_url_t::port The TCP port number of the service providing the URL [ftp, gsiftp, http, https, ldap, x-nexus]. char* globus_url_t::url_path The path name of the resource on the service providing the URL. [ftp, gsiftp, http, https] char* globus_url_t::dn The distinguished name for the base of an LDAP search. [ldap] char* globus_url_t::attributes The list of attributes which should be returned from an LDAP search. [ldap] char* globus_url_t::scope The scope of an LDAP search. [ldap] char* globus_url_t::filter The filter to be applied to an LDAP search [ldap]. char* globus_url_t::url_specific_part An unparsed string containing the remaining text after the optional host and port of an unknown URL, or the contents of a x-gass-cache URL [x-gass-cache, unknown]. Author Generated automatically by Doxygen for globus common from the source code. Version 14.7 Tue Nov 27 2012 globus_url_t(3)
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