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Top Forums Shell Programming and Scripting Reading from file bash command Post 303003202 by MadeInGermany on Saturday 9th of September 2017 06:59:32 AM
Old 09-09-2017
I do not see the problem.?
Read enough fields, because joining is easier than splitting.
An exercise for demonstration
Code:
while read  id sample platform R1 R2 gene1 gene2 gene3 junk
do
  echo "----"
  echo "process non-empty genes"
  for i in $gene1 $gene2 $gene3; do echo "$i"; done
  echo "process all 3 genes"
  for i in "$gene1" "$gene2" "$gene3"; do echo "$i"; done
done < samples.txt

 

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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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