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Full Discussion: Reading from file bash command
Top Forums Shell Programming and Scripting Reading from file bash command Post 303003159 by nans on Friday 8th of September 2017 07:26:40 AM
Old 09-08-2017
Reading from file bash command
Hello, I have a file in the following format

Code:
id sample platform R1 R2 gene1 gene2 gene3
1       abc     llumina       R1_001.fastq.gz      R2_001.fastq.gz   apoe    prnpp    asp
2       def     llumina       R1_001.fastq.gz      R2_001.fastq.gz   apoe    prnpp    
3       ghi     llumina       R1_001.fastq.gz      R2_001.fastq.gz   apoe

The first 6 columns are always filled, the last two columns are only for some entries. So I have a main script that reads this file to process these ids further. I generally use

Code:
while id sample platform R1 R2 gene1
do
<mainscript.sh>
done < samples.txt

But how can I include the last two columns as well to run the command as many entries under the variable gene2 and gene3 are empty.

This is what i have tried so far to read all the lines in the file and if variable under gene2 and/or gene3 are empty, to move to the next line

Code:
while read  id sample platform R1 R2 gene1 gene2 gene3
do
echo "$id $sample $gene1 $gene2" | {
        read  id sample platform R1 R2 gene1 gene2
        [ -z "$gene2" ] && continue
        for i in $gene2; do eval echo "\"$i\""; done
 }
 
 done < samples.txt

I could do it for gene2 but wasnt able to implement it for gene3

any suggestions would be helpful

thank you
 

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LEARN ABOUT XFREE86

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)

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