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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 CENTOS

bashbug-64

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)
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