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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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gv(3python)															       gv(3python)

NAME

       gv_python - graph manipulation in python

SYNOPSIS

       #!/usr/bin/python
       import gv

USAGE

INTRODUCTION

       gv_python is a dynamically loaded extension for python that provides access to the graph facilities of graphviz.

COMMANDS

       New graphs

       New empty graph
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	      graph_handle gv.digraph (name);
	      graph_handle gv.strictgraph (name);
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       Add new subgraph to existing graph
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       New nodes

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       New edges

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	      edge_handle gv.edge (tail_node_handle, head_node_handle);

       Add a new edge between an existing tail node, and a named head node which will be induced in the graph if it doesn't already exist
	      edge_handle gv.edge (tail_node_handle, head_name);

       Add a new edge between an existing head node, and a named tail node which will be induced in the graph if it doesn't already exist
	      edge_handle gv.edge (tail_name, head_node_handle);

       Add a new edge between named tail  and head nodes which will be induced in the graph if they don't already exist
	      edge_handle gv.edge (graph_handle, tail_name, head_name);

       Setting attribute values

       Set value of named attribute of graph/node/edge - creating attribute if necessary
	      string gv.setv (graph_handle, attr_name, attr_value);
	      string gv.setv (node_handle, attr_name, attr_value);
	      string gv.setv (edge_handle, attr_name, attr_value);

       Set value of existing attribute of graph/node/edge (using attribute handle)
	      string gv.setv (graph_handle, attr_handle, attr_value);
	      string gv.setv (node_handle, attr_handle, attr_value);
	      string gv.setv (edge_handle, attr_handle, attr_value);

       Getting attribute values

       Get value of named attribute of graph/node/edge
	      string gv.getv (graph_handle, attr_name);
	      string gv.getv (node_handle, attr_name);
	      string gv.getv (edge_handle, attr_name);

       Get value of attribute of graph/node/edge (using attribute handle)
	      string gv.getv (graph_handle, attr_handle);
	      string gv.getv (node_handle, attr_handle);
	      string gv.getv (edge_handle, attr_handle);

       Obtain names from handles
	      string gv.nameof (graph_handle);
	      string gv.nameof (node_handle);
	      string gv.nameof (attr_handle);

       Find handles from names
	      graph_handle gv.findsubg (graph_handle, name);
	      node_handle gv.findnode (graph_handle, name);
	      edge_handle gv.findedge (tail_node_handle, head_node_handle);
	      attribute_handle gv.findattr (graph_handle, name);
	      attribute_handle gv.findattr (node_handle, name);
	      attribute_handle gv.findattr (edge_handle, name);

       Misc graph navigators returning handles
	      node_handle gv.headof (edge_handle);
	      node_handle gv.tailof (edge_handle);
	      graph_handle gv.graphof (graph_handle);
	      graph_handle gv.graphof (edge_handle);
	      graph_handle gv.graphof (node_handle);
	      graph_handle gv.rootof (graph_handle);

       Obtain handles of proto node/edge for setting default attribute values
	      node_handle gv.protonode (graph_handle);
	      edge_handle gv.protoedge (graph_handle);

       Iterators

       Iteration termination tests
	      bool gv.ok (graph_handle);
	      bool gv.ok (node_handle);
	      bool gv.ok (edge_handle);
	      bool gv.ok (attr_handle);

       Iterate over subgraphs of a graph
	      graph_handle gv.firstsubg (graph_handle);
	      graph_handle gv.nextsubg (graph_handle, subgraph_handle);

       Iterate over supergraphs of a graph (obscure and rarely useful)
	      graph_handle gv.firstsupg (graph_handle);
	      graph_handle gv.nextsupg (graph_handle, subgraph_handle);

       Iterate over edges of a graph
	      edge_handle gv.firstedge (graph_handle);
	      edge_handle gv.nextedge (graph_handle, edge_handle);

       Iterate over outedges of a graph
	      edge_handle gv.firstout (graph_handle);
	      edge_handle gv.nextout (graph_handle, edge_handle);

       Iterate over edges of a node
	      edge_handle gv.firstedge (node_handle);
	      edge_handle gv.nextedge (node_handle, edge_handle);

       Iterate over out-edges of a node
	      edge_handle gv.firstout (node_handle);
	      edge_handle gv.nextout (node_handle, edge_handle);

       Iterate over head nodes reachable from out-edges of a node
	      node_handle gv.firsthead (node_handle);
	      node_handle gv.nexthead (node_handle, head_node_handle);

       Iterate over in-edges of a graph
	      edge_handle gv.firstin (graph_handle);
	      edge_handle gv.nextin (node_handle, edge_handle);

       Iterate over in-edges of a node
	      edge_handle gv.firstin (node_handle);
	      edge_handle gv.nextin (graph_handle, edge_handle);

       Iterate over tail nodes reachable from in-edges of a node
	      node_handle gv.firsttail (node_handle);
	      node_handle gv.nexttail (node_handle, tail_node_handle);

       Iterate over nodes of a graph
	      node_handle gv.firstnode (graph_handle);
	      node_handle gv.nextnode (graph_handle, node_handle);

       Iterate over nodes of an edge
	      node_handle gv.firstnode (edge_handle);
	      node_handle gv.nextnode (edge_handle, node_handle);

       Iterate over attributes of a graph
	      attribute_handle gv.firstattr (graph_handle);
	      attribute_handle gv.nextattr (graph_handle, attr_handle);

       Iterate over attributes of an edge
	      attribute_handle gv.firstattr (edge_handle);
	      attribute_handle gv.nextattr (edge_handle, attr_handle);

       Iterate over attributes of a node
	      attribute_handle gv.firstattr (node_handle);
	      attribute_handle gv.nextattr (node_handle, attr_handle);

       Remove graph objects
	      bool gv.rm (graph_handle);
	      bool gv.rm (node_handle);
	      bool gv.rm (edge_handle);

       Layout

       Annotate a graph with layout attributes and values using a specific layout engine
	      bool gv.layout (graph_handle, string engine);

       Render

       Render a layout into attributes of the graph
	      bool gv.render (graph_handle);

       Render a layout to stdout
	      bool gv.render (graph_handle, string format);

       Render to an open file
	      bool gv.render (graph_handle, string format, channel fout);

       Render a layout to an unopened file by name
	      bool gv.render (graph_handle, string format, string filename);

       Render to an open channel
	      bool gv.renderchannel (graph_handle, string format, string channelname);

       Render to a string result
	      gv.renderresult (graph_handle, string format, string outdata);

       Render a layout to a malloc'ed string, to be free'd by the caller

       (deprecated - too easy to leak memory)

       (still needed for "eval [gv::renderdata $G tk]" )
	      string gv.renderdata (graph_handle, string format);

       Writing graph back to file
	      bool gv.write (graph_handle, string filename);
	      bool gv.write (graph_handle, channel);

KEYWORDS

       graph, dot, neato, fdp, circo, twopi, python.

								  11 January 2014						       gv(3python)
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