Reading from file bash command Post: 303003163

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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

09-08-2017

Registered User

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.

jim mcnamara

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LEARN ABOUT LINUX

rbash

RBASH(1)						      General Commands Manual							  RBASH(1)

NAME

       rbash - restricted bash, see bash(1)

RESTRICTED SHELL

       If  bash  is  started with the name rbash, or the -r option is supplied at invocation, the shell becomes restricted.  A restricted shell is
       used to set up an environment more controlled than the standard shell.  It behaves identically to bash with the exception that the  follow-
       ing are disallowed or not performed:

       o      changing directories with cd

       o      setting or unsetting the values of SHELL, PATH, ENV, or BASH_ENV

       o      specifying command names containing /

       o      specifying a file name containing a / as an argument to the .  builtin command

       o      specifying a filename containing a slash as an argument to the -p option to the hash builtin command

       o      importing function definitions from the shell environment at startup

       o      parsing the value of SHELLOPTS from the shell environment at startup

       o      redirecting output using the >, >|, <>, >&, &>, and >> redirection operators

       o      using the exec builtin command to replace the shell with another command

       o      adding or deleting builtin commands with the -f and -d options to the enable builtin command

       o      using the enable builtin command to enable disabled shell builtins

       o      specifying the -p option to the command builtin command

       o      turning off restricted mode with set +r or set +o restricted.

       These restrictions are enforced after any startup files are read.

       When a command that is found to be a shell script is executed, rbash turns off any restrictions in the shell spawned to execute the script.

SEE ALSO

       bash(1)

GNU Bash-4.0							    2004 Apr 20 							  RBASH(1)

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