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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 DEBIAN

lfc-dli

LFC-DLI(8)						    LFC Administrator Commands							LFC-DLI(8)

NAME

       lfc-dli - start the LFC Data Location Interface server

SYNOPSIS

       lfc-dli [ -l log_file ]

DESCRIPTION

       The  lfc-dli  command  starts  the  LFC	Data  Location	Interface  server.   This  command  is	usually  executed  at  system startup time
       (/etc/rc.local).  This will create a pool of threads, look for requests and pass them to the LFC.  When a request has been  completed,  the
       thread becomes idle until it is allocated to another request.

       All error messages and statistical information are kept in a log.

       The  Data  Location  Interface server listen port number can be defined on client hosts and on the server itself in either of the following
       ways:

	      setting an environment variable DLI_PORT

		     setenv DLI_PORT 8085

	      an entry in /etc/shift.conf like:

		     DLI  PORT 8085

       If none of these methods is used, the default port number is taken from the definition of DLI_PORT in dli_server.h.

       In the log each entry has a timestamp.  For each user request there is one message giving information about the	requestor  (hostname)  and
       one message DLI98 giving the request itself.  The completion code of the request is also logged.

OPTIONS

       -l log_file
	      Specifies a different path for the LFC Data Location Interface server log file.  The special value syslog will send the log messages
	      to the system logger syslogd.

FILES

       /var/log/lfc-dli/log

EXAMPLES

       Here is a small log:
	      05/18 16:27:21  1942 dli: started
	      05/18 22:10:33  1942,0 listReplicas: request from lxb2016.cern.ch
	      05/18 22:10:33  1942,0 listReplicas: DLI98 - listReplicas lfn:/grid/dteam/foo888
	      05/18 22:10:34  1942,0 listReplicas: returns 0
	      05/18 22:12:10  1942,0 listReplicas: request from lxb2016.cern.ch
	      05/18 22:12:10  1942,0 listReplicas: DLI98 - listReplicas guid:41b20a76-2287-4f81-9750-7e2eb4d199c8
	      05/18 22:12:11  1942,0 listReplicas: returns 0

SEE ALSO

       Clogit(3), lfc-server(8)

LCG
								      $Date$								LFC-DLI(8)
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