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 X11R4

libbash

LIBBASH(7)							  libbash Manual							LIBBASH(7)

NAME

     libbash -- A bash shared libraries package.

DESCRIPTION

     libbash  is  a package that enables bash dynamic-like shared libraries. Actually its a tool for managing bash scripts whose functions you may
     want to load and use in scripts of your own.

     It contains a 'dynamic loader' for the shared libraries ( ldbash(1)), a configuration tool (ldbashconfig(8)), and some libraries.

     Using ldbash(1) you are able to load loadable bash libraries, such as getopts(1) and hashstash(1).  A bash shared library that can be  loaded
     using
     ldbash(1) must answer 4 requirments:

     1.     It must be installed in $LIBBASH_PREFIX/lib/bash (default is /usr/lib/bash).

     2.     It must contain a line that begins with '#EXPORT='.  That line will contain (after the '=') a list of functions that the library
	    exports.  I.e. all the function that will be usable after loading that library will be listed in that line.

     3.     It must contain a line that begins with '#REQUIRE='.  That line will contain (after the '=') a list of bash libraries that are
	    required for our library.  I.e. every bash library that is in use in our bash library must be listed there.

     4.     The library must be listed (For more information, see ldbashconfig(8)).

   Basic guidelines for writing library of your own:
     1.     Be aware, that your library will be actually sourced. So, basically, it should contain (i.e define) only functions.

     2.     Try to declare all variables intended for internal use as local.

     3.     Global variables and functions that are intended for internal use (i.e are not defined in '#EXPORT=') should begin with:
		  __<library_name>_
	    For example, internal function myfoosort of hashstash library should be named as
		  __hashstash_myfoosort
	    This helps to avoid conflicts in global name space when using libraries that come from different vendors.

     4.     See html manual for full version of this guide.

AUTHORS

     Hai Zaar <haizaar@haizaar.com>
     Gil Ran <ril@ran4.net>

SEE ALSO

     ldbash(1), ldbashconfig(8), getopts(1), hashstash(1) colors(1) messages(1) urlcoding(1) locks(1)

Linux								       Epoch								     Linux

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