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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

update-python-modules

UPDATE-PYTHON-MODULES(8)				      System Manager's Manual					  UPDATE-PYTHON-MODULES(8)

NAME

       update-python-modules - byte-compile python modules

SYNOPSIS

       update-python-modules [options] [package.public [...]]

DESCRIPTION

       The update-python-modules command is part of the python-support bundle.

       update-python-modules  is  responsible for the byte-compilation of python modules. When used in byte-compilation mode, it will byte-compile
       modules references in the files given on the command line. When used in	installation  mode,  it  will  byte-compile  them  once  for  each
       installed python version, and will make them available for all of them.

       At  each  invocation,  with  or without arguments, update-python-modules will check for installed python versions, and will build or remove
       modules according to new or removed versions since the last time it was run.

ARGUMENTS

       Arguments must be files or directories located in the /usr/share/python-support directory. Depending on their extension, they  are  treated
       differently.

       package.public
	      A file listing public modules to install for each version. These modules must lie in /usr/share/pyshared or /usr/lib/pyshared.

       package.private
	      A file listing private modules to byte-compile for one Python version.

       package/
	      A legacy directory hierarchy of public modules. The C extensions and portions that change with the Python version are to be found in
	      /usr/lib/python-support/pythonX.Y/package/.

       package.dirs
	      A legacy file listing directories where to find private modules.

OPTIONS

       -h, --help
	      Show summary of options.

       -v, --verbose
	      Detail all actions while they are performed.

       -b, --bytecompile
	      Only accept to work on private modules. When given this option, update-python-modules will fail if passed references to public  mod-
	      ules.

       -i, --install
	      Only  accept  to work on public modules. When given this option, update-python-modules will fail if passed references to public mod-
	      ules.

       -c, --clean
	      Clean modules instead of installing them.

       -a, --rebuild-all
	      Rebuild all private modules. This is necessary when the default python version was changed, for example.

       -f, --force-rebuild-all
	      Clean all modules (public and private), and rebuild them.

FILES

       /usr/lib/pymodules/pythonX.Y/
	      These directories contain the byte-compiled modules for version pythonX.Y.

SEE ALSO

       /usr/share/doc/python-support/README.gz

AUTHOR

       Josselin Mouette <joss@debian.org>.

								    18 Feb 2009 					  UPDATE-PYTHON-MODULES(8)
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