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Full Discussion: UNIX command to select the best edge values from a network file
Top Forums UNIX for Beginners Questions & Answers UNIX command to select the best edge values from a network file Post 303045006 by Sanchari on Tuesday 10th of March 2020 06:16:47 PM
Old 03-10-2020
UNIX command to select the best edge values from a network file
I have a tab-delimited data representing network data (undirected). Among the duplicated edges, I wanted to select those edges for which I have the higher absolute value of the log values.
I have written a code in python, but its taking a lot of time. I would be grateful if someone helps me with an awk command. Kindly note, the network is undirected, i.e. A--B and B--A are duplicate edges. My original file has a large number of columns, I have given a simplified test data

Test data



Code:
     Gene1    Gene2    Log
    AT1G01020    AT1G01010    1.682708
    AT1G01020    AT1G01010    -1.90043
    AT1G01020    AT1G01010    -1.832192
    AT1G01070    AT1G01060    -0.591932
    AT1G01070    AT1G01060    -1.204241
    AT1G01073    AT1G01070    0.790549
    AT1G01060    AT1G01070    1.214972

Expected Output

Code:
    AT1G01020    AT1G01010    -1.90043
    AT1G01070    AT1G01060    1.214972
    AT1G01073    AT1G01070    0.790549

Code:
gene_table=file1.readlines() # In the real file, j[12]=Gene1, j[13]=Gene2 and j[27]=log value
lfc=[]
for j in gene_table:
    j=j.split("\t")
    j[12]=j[12].strip()
    j[13]=j[13].strip()
    lfc=[]
    int_list=[]
    lfc.append(float(j[27]))
    int_list.append(j[0])
    dict_int={}
    for k in gene_table:
        k=k.split("\t")
        k[12]=k[12].strip()
        k[13]=k[13].strip()
        if (j[0]!=k[0]) and ((j[12]==k[12] and j[13]==k[13]) or (j[12]==k[13] and j[12]==k[13])):
            lfc.append(float(k[27]))
    dict_int=dict(zip(int_list, lfc))
    x=max(lfc, key=abs)
    #print x
    listOfKeys = [key  for (key, value) in dict_int.items() if value == x]
    print listOfKeys

Last edited by Scrutinizer; 03-11-2020 at 12:29 AM..
 

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LEARN ABOUT CENTOS

locale::codes::langfam

Locale::Codes::LangFam(3)				User Contributed Perl Documentation				 Locale::Codes::LangFam(3)

NAME

       Locale::Codes::LangFam - standard codes for language extension identification

SYNOPSIS

	  use Locale::Codes::LangFam;

	  $lext = code2langfam('apa');		       # $lext gets 'Apache languages'
	  $code = langfam2code('Apache languages');    # $code gets 'apa'

	  @codes   = all_langfam_codes();
	  @names   = all_langfam_names();

DESCRIPTION

       The "Locale::Codes::LangFam" module provides access to standard codes used for identifying language families, such as those as defined in
       ISO 639-5.

       Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default ISO 639-5
       language family codes will be used.

SUPPORTED CODE SETS

       There are several different code sets you can use for identifying language families. A code set may be specified using either a name, or a
       constant that is automatically exported by this module.

       For example, the two are equivalent:

	  $lext = code2langfam('apa','alpha');
	  $lext = code2langfam('apa',LOCALE_LANGFAM_ALPHA);

       The codesets currently supported are:

       alpha
	   This is the set of three-letter (lowercase) codes from ISO 639-5 such as 'apa' for Apache languages.

	   This is the default code set.

ROUTINES

       code2langfam ( CODE [,CODESET] )
       langfam2code ( NAME [,CODESET] )
       langfam_code2code ( CODE ,CODESET ,CODESET2 )
       all_langfam_codes ( [CODESET] )
       all_langfam_names ( [CODESET] )
       Locale::Codes::LangFam::rename_langfam  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Codes::LangFam::add_langfam  ( CODE ,NAME [,CODESET] )
       Locale::Codes::LangFam::delete_langfam  ( CODE [,CODESET] )
       Locale::Codes::LangFam::add_langfam_alias  ( NAME ,NEW_NAME )
       Locale::Codes::LangFam::delete_langfam_alias  ( NAME )
       Locale::Codes::LangFam::rename_langfam_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangFam::add_langfam_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangFam::delete_langfam_code_alias  ( CODE [,CODESET] )
	   These routines are all documented in the Locale::Codes::API man page.

SEE ALSO

       Locale::Codes
	   The Locale-Codes distribution.

       Locale::Codes::API
	   The list of functions supported by this module.

       http://www.loc.gov/standards/iso639-5/id.php
	   ISO 639-5 .

AUTHOR

       See Locale::Codes for full author history.

       Currently maintained by Sullivan Beck (sbeck@cpan.org).

COPYRIGHT

	  Copyright (c) 2011-2013 Sullivan Beck

       This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

perl v5.16.3							    2013-02-27						 Locale::Codes::LangFam(3)
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