Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Reading from file bash command
Top Forums Shell Programming and Scripting Reading from file bash command Post 303003163 by jim mcnamara on Friday 8th of September 2017 08:29:04 AM
Old 09-08-2017
This statement means that if there is no gene2 then there cannot be a gene3 read:
Code:
 [ -z "$gene2" ] && continue

When you use the read statement you have to have all fields there in order to get gene3.

Otherwise gene3 is an "empty" variable. Or the same can happen for gene2.

You can create dummy values for those variables if they are empty, but since you have a separate script processing things that could affect the output of that script.

Try creating an intermediate file with dummy variables, let's use the word 'dummy' for the values of empties. This is awk, the output file will be called tmp.tmp which is what your script will have to use for input.

This could also be set up writing to a pipe which your existing script reads.
Code:
awk '{
        # check to see what type of line we have, 
        # if  col 1 is a number then we have to play the dummy game
        if( int($1) !=0)
        {
            if(NF==6) { $7="dummy"; $8="dummy" }
            if(NF==7) { $8="dummy" }
         }
        print $0 
       }'  inputfile > tmp.tmp

So the last 2 fields in tmp.tmp can be a real value, or just fiber filler: "dummy", but there will always be 8 fields. The last two fields cannot be blank or bash will not read them into a variable.
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Bash: Reading 2 arguments from a command line

If no arguments are entered I wanna be able to read 2 arguments, i have done like this but it doesnt work: x=0 until #loop starts do if ; then echo No arguments were entered, please enter 2 arguments. read $1 $2 elif || ; then echo $#... (0 Replies)
Discussion started by: Vozx
0 Replies

2. Shell Programming and Scripting

bash: reading filenames from file

Hi, I'm trying to write a script that reads filenames from a file and use these filenames in a loop. The filenames are all on one line and the problem is that these filenames have wildcards like * and braces like in them. Right now what I'm doing is something like this: echo "reading from... (0 Replies)
Discussion started by: warp17
0 Replies

3. Shell Programming and Scripting

Reading lines from a file, using bash, "at" command

Hi. I have the script shown below. If I execute it form the command line it seems to work properly, but when I fun it using the unix "at" command "at -m now < ./kill-at-job.sh" It appears to hang. Below is the script, the input file, and the execution as reported in the e-mail from the "at"... (3 Replies)
Discussion started by: jbsimon000
3 Replies

4. Shell Programming and Scripting

Problem in reading file (bash)

i get a name from user first name : last name, in this format. Now i am saving this to a file. what i want is, I do not want to save any name if I already have one entry o that same name..what should i do for example user give robert fernandez this will save in file as robert:fernandez. if... (5 Replies)
Discussion started by: Learnerabc
5 Replies

5. Shell Programming and Scripting

Help in reading a cv file in bash

Hi All, I am trying to read a .csv file which has some 6 columns. Eg: samp.csv one, two, three, four six, seven, eight, nine I used the following code, for line in `cat samp.csv` do echo "$line" done It displays every comma seperated values in each line like, one,... (1 Reply)
Discussion started by: johnwilliams.sp
1 Replies

6. Shell Programming and Scripting

Bash: Reading a file and assigning variables from file

I have a file that has four values on each line and I'd like to give each column a variable name and then use those values in each step of a loop. In bash, I believe you could use a while loop to do this or possibly a cat command, but I am super new to programming and I'm having trouble decoding... (2 Replies)
Discussion started by: ccorder22
2 Replies

7. Shell Programming and Scripting

Reading command line options from bash script

I have the following code and I am calling it using ./raytrac.bash -u and getting problems. For some reason opt_usage is still 0. opt_usage=0 iarg=0 narg=$# while (($iarg < $narg)) do (( iarg = $iarg + 1 )) arg=$argv usrInputFlag=`echo $arg | awk '/=/ {print 1}; ! /=/... (22 Replies)
Discussion started by: kristinu
22 Replies

8. Shell Programming and Scripting

Reading a text file using bash

I've a file in linux with following text: ;ip address hostname put-location alt-put-location tftpserver 192.168.1.1 r01-lab1-net /mnt/nas1/fgbu/ /opt/fgbu/devicebackup 192.168.1.254Now I want to read these values and assign them to particular variables... (6 Replies)
Discussion started by: kashif.live
6 Replies

9. UNIX for Beginners Questions & Answers

Reading a file from a different directory in a Bash script

Hi all, Given here under a section of a script I am using. SIMDIR="/home/Ins/forces" cd $SIMDIR for file in `ls *.forces` do basename=`echo $file | sed 's/\.*$//'` extname=`echo $file | sed 's/*\(*\)\.\(.*\)/\2\1/'` echo "Processing file: "$basename python convert.py... (4 Replies)
Discussion started by: Theo Score
4 Replies

10. UNIX for Beginners Questions & Answers

Bash Variable scope - while loop while reading from a file

Cope sample1: test.sh i=0 echo " Outside loop i = $i " while do i=$(( $i + 1)) echo "Inside loop i = $i " done echo " Out of loop i is : $i " When run output : Outside loop i = 0 Inside loop i = 1 Inside loop i = 2 Inside loop i = 3 Inside loop i = 4 Inside loop i = 5 Inside... (8 Replies)
Discussion started by: Adarshreddy01
8 Replies

LEARN ABOUT CENTOS

bashbug

BASHBUG(1)						      General Commands Manual							BASHBUG(1)

NAME

       bashbug - report a bug in bash

SYNOPSIS

       bashbug [--version] [--help] [email-address]

DESCRIPTION

       bashbug	is  a shell script to help the user compose and mail bug reports concerning bash in a standard format.	bashbug invokes the editor
       specified by the environment variable EDITOR on a temporary copy of the bug report format outline. The user must fill  in  the  appropriate
       fields  and  exit  the  editor.	 bashbug  then	mails the completed report to bug-bash@gnu.org, or email-address.  If the report cannot be
       mailed, it is saved in the file dead.bashbug in the invoking user's home directory.

       The bug report format outline consists of several sections.  The first section provides information about the  machine,	operating  system,
       the  bash  version, and the compilation environment.  The second section should be filled in with a description of the bug.  The third sec-
       tion should be a description of how to reproduce the bug.  The optional fourth section is for a proposed fix.  Fixes are encouraged.

ENVIRONMENT

       bashbug will utilize the following environment variables if they exist:

       EDITOR Specifies the preferred editor. If EDITOR is not set, bashbug defaults to emacs.

       HOME   Directory in which the failed bug report is saved if the mail fails.

       TMPDIR Directory in which to create temporary files and directories.

SEE ALSO

       bash(1)

AUTHORS

       Brian Fox, Free Software Foundation
       bfox@gnu.org

       Chet Ramey, Case Western Reserve University
       chet@po.cwru.edu

GNU Bash-4.0							   1998 July 30 							BASHBUG(1)
All times are GMT -4. The time now is 07:19 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy