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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-getacl

LFC-GETACL(1)							 LFC User Commands						     LFC-GETACL(1)

NAME

       lfc-getacl - get LFC directory/file access control lists

SYNOPSIS

       lfc-getacl [-a] [-d] path...

DESCRIPTION

       lfc-getacl gets the Access Control List associated with a LFC directory/file.  For each path, it  displays the file name, owner, the group,
       and the Access Control List (ACL) if present. If a directory has a default ACL, lfc-getacl also displays the  default  ACL.  Regular  files
       cannot have default ACLs.

       The output looks like:

	    # file: filename
	    # owner: username
	    # group: groupname
	    user::perm
	    user:uid:perm
	    group::perm
	    group:gid:perm
	    mask:perm
	    other:perm
	    default:user::perm
	    default:user:uid:perm
	    default:group::perm
	    default:group:gid:perm
	    default:mask:perm
	    default:other:perm

       The  first  "user" entry gives the permissions granted to the owner of the file.  The following "user" entries show the permissions granted
       to specific users, they are sorted in ascending order of uid.  The first "group" entry gives the permissions granted to the group owner	of
       the  file.   The following "group" entries show the permissions granted to specific groups, they are sorted in ascending order of gid.  The
       "mask" entry is the maximum permission granted to specific users or groups.  It does not affect the "owner" and "other"	permissions.   The
       "mask"  entry must be present if there are specific "user" or "group" entries.  "default" entries associated with a directory are inherited
       as access ACL by the files or sub-directories created in that directory. The umask is not used.	Sub-directories also inherit  the  default
       ACL as default ACL.  As soon as there is one default ACL entry, the 3 default ACL base entries (default user, default group, default other)
       must be present.

       The entry processing conforms to the Posix 1003.1e draft standard 17.

       path   specifies the LFC pathname.  If path does not start with /, it is prefixed by the content of the LFC_HOME environment variable.

       uid    is displayed as the username if known else as the numeric id.

       gid    is displayed as the groupname if known else as the numeric id.

       perm   is expressed as a combination of characters rwx-

OPTIONS

       -a     only display the access ACL.

       -d     only display the default ACL.

EXAMPLES

       lfc-getacl /grid/atlas/test/file.log/d2

       # file: /grid/atlas/test/file.log/d2
       # owner: baud
       # group: c3
       user::rwx
       group::r-x	       #effective:r-x
       other::r-x
       default:user::rwx
       default:group::r-x
       default:other::r-x

EXIT STATUS

       This program returns 0 if the operation was successful or >0 if the operation failed.

SEE ALSO

       Castor_limits(4), lfc_chmod(3), lfc_chown(3)

AUTHOR

       LCG Grid Deployment Team

LFC
							   $Date: 2005/03/02 08:32:12 $ 					     LFC-GETACL(1)
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