Login or Register to Ask a Question and Join Our Community

Sponsored Content
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..
 

8 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

How to select a particular media from the printer with a UNIX command

Problem Overview: We have a scheduler that prints report on any of the network printer. Problem Statement: We need to find a UNIX command that picks up either A4, legal or letter size paper form the printer. I found out a command but it's not working on our environment. ... (3 Replies)
Discussion started by: HelpMeOUt
3 Replies

2. Shell Programming and Scripting

Select distinct values from a flat file

Hi , I have a similar problem. Please can anyone help me with a shell script or a perl. I have a flat file like this fruit country apple germany apple india banana pakistan banana saudi mango india I want to get a output like fruit country apple ... (7 Replies)
Discussion started by: smalya
7 Replies

3. Shell Programming and Scripting

Identify high values "ÿ" in a text file using Unix command

I have high values (such as ÿÿÿÿ) in a text file contained in an Unix AIX server. I need to identify all the records which are having these high values and also get the position/column number in the record structure if possible. Is there any Unix command by which this can be done to : 1.... (5 Replies)
Discussion started by: devina
5 Replies

4. Shell Programming and Scripting

Running a select script through UNIX and sending output to file

Hi, (Oracle, AIX) I have googled this and searched this forum, however I haven't had much luck with an answer and have tried several different things. Basically I have a SQL select statement which generates a whole load of UPDATE statements, I want to run the select statement via... (13 Replies)
Discussion started by: dbchud
13 Replies

5. Shell Programming and Scripting

Unix command to select first few characters and last character of a line

I have a huge file and I want to select first 10 charcters and last 2 characters of everyline and than will filter the unique line. I know, it must be easy bt I am new to unix scripting:) Ex. I have file as below and need to e3kbaird and last 2 characters. and than unique records. ... (3 Replies)
Discussion started by: Sanjeev Yadav
3 Replies

6. Shell Programming and Scripting

Comparing multiple network files (edge lists)

I want to compare 4 edge-lists to basically see if an edge is present in all 4 networks. The issue is that an edge A-B in one file can be present as B-A in another file. Example: Input 1: net1.txt A B 0.1 C D 0.65 D E 0.9 E A 0.7 Input 2: net2.txt A Z 0.1 C D 0.65 E D 0.9 E A... (1 Reply)
Discussion started by: Sanchari
1 Replies

7. Shell Programming and Scripting

UNIX command -Filter rows in fixed width file based on column values

Hi All, I am trying to select the rows in a fixed width file based on values in the columns. I want to select only the rows if column position 3-4 has the value AB I am using cut command to get the column values. Is it possible to check if cut -c3-4 = AB is true then select only that... (2 Replies)
Discussion started by: ashok.k
2 Replies

8. Shell Programming and Scripting

Split a content in a file with specific interval base on the delimited values using UNIX command

Hi All, we have a requirement to split a content in a text file every 5 rows and write in a new file . conditions: if 5th line falls between center of the statement . it should look upto after ";" files are below format: 1 UPDATE TABLE TEST1 SET VALUE ='AFDASDFAS' 2 WHERE... (3 Replies)
Discussion started by: KK230689
3 Replies

LEARN ABOUT DEBIAN

python-config

PYTHON-CONFIG(1)					      General Commands Manual						  PYTHON-CONFIG(1)

NAME

       python-config - output build options for python C/C++ extensions or embedding

SYNOPSIS

       python-config  [ --prefix ] [ --exec-prefix ] [ --includes ] [ --libs ] [ --cflags ] [ --ldflags ] [ --extension-suffix ] [ --configdir ] [
       --help ]

DESCRIPTION

       python-config helps compiling and linking programs, which embed the Python interpreter, or extension modules that can be loaded dynamically
       (at run time) into the interpreter.

OPTIONS

       --cflags
	      print the C compiler flags.

       --ldflags
	      print the flags that should be passed to the linker.

       --includes
	      similar to --cflags but only with -I options (path to python header files).

       --libs similar to --ldflags but only with -l options (used libraries).

       --prefix
	      prints the prefix (base directory) under which python can be found.

       --exec-prefix
	      print the prefix used for executable program directories (such as bin, sbin, etc).

       --extension-suffix
	      print suffix used for extension modules (including the _d modified for debug builds).

       --configdir
	      prints the path to the configuration directory under which the Makefile, etc. can be found).

       --help print the usage message.

EXAMPLES

       To build the singe-file c program prog against the python library, use

	      gcc $(python-config --cflags --ldflags) progr.cpp -o progr.cpp

       The same in a makefile:

	      CFLAGS+=$(shell python-config --cflags)
	      LDFLAGS+=$(shell python-config --ldflags)
	      all: progr

       To build a dynamically loadable python module, use

	      gcc $(python-config --cflags --ldflags) -shared -fPIC progr.cpp -o progr.so

SEE ALSO

       python (1)
       http://docs.python.org/extending/extending.html
       /usr/share/doc/python/faq/extending.html

AUTHORS

       This manual page was written by Johann Felix Soden <johfel@gmx.de> for the Debian project (and may be used by others).

								 November 27, 2011						  PYTHON-CONFIG(1)
All times are GMT -4. The time now is 02:22 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy