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Top Forums UNIX for Beginners Questions & Answers How to insert a string and variable at specified position in command in bash? Post 303042115 by cmccabe on Sunday 15th of December 2019 10:06:38 AM
Old 12-15-2019
How to insert a string and variable at specified position in command in bash?

I currently have a loop that reads all .bam files in a directory (wont always be 4 like in this example,
into $id. What I am trying to do, unsucessfully, is create specific new lines in an exsisting command using
each $id. Each new line would be:
Code:
--bam ${id} \

Tried
Code:
p=$dir
/path/to/xxx.py \
text="$(--bam ${id \})"
text="${text:0:p}j${text:p}"  ## insert text for each $p
     --ref /path/to/file \
     --run /ptah/to/data

directory
Code:
s1.bam
s2.bam
s3.bam
s4.bam

standard command
Code:
/path/to/xxx.py \
     --bam ${id}.bam \
     --ref /path/to/file \
     --run /ptah/to/data

desired command
Code:
/path/to/xxx.py \
     --bam s1.bam \
	 --bam s2.bam \
	 --bam s3.bam \
	 --bam s4.bam \
	 --ref /path/to/file \
     --run /path/to/data


Last edited by cmccabe; 12-15-2019 at 11:08 AM.. Reason: fixed format
 

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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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