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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 303042117 by RudiC on Sunday 15th of December 2019 10:34:29 AM
Old 12-15-2019
Not sure I fully understand, and your "Tried" block seems to be gobbledigook, but how about
Code:
while IFS="" read -r LN
  do    [ "$LN" = "${LN##*id}" ] && echo "$LN" || for FN in *.bam
                                                    do echo "     -- bam $FN \\"
                                                    done
  done < file
/path/to/xxx.py \
     -- bam s1.bam \
     -- bam s2.bam \
     -- bam s3.bam \
     -- bam s4.bam \
     --ref /path/to/file \
     --run /ptah/to/data


EDIT: or
Code:
ls *.bam | awk 'NR == FNR {T = T DL "     --bam " $0 " \\"; DL = RS; next} /id/ {print T; next} 1' - file


Last edited by RudiC; 12-15-2019 at 11:52 AM..
This User Gave Thanks to RudiC For This Post:
 

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SYSTEM(3)						     Linux Programmer's Manual							 SYSTEM(3)

NAME
system - execute a shell command SYNOPSIS
#include <stdlib.h> int system(const char *string); DESCRIPTION
system() executes a command specified in string by calling /bin/sh -c string, and returns after the command has been completed. During execution of the command, SIGCHLD will be blocked, and SIGINT and SIGQUIT will be ignored. RETURN VALUE
The value returned is -1 on error (e.g. fork failed), and the return status of the command otherwise. This latter return status is in the format specified in wait(2). Thus, the exit code of the command will be WEXITSTATUS(status). In case /bin/sh could not be executed, the exit status will be that of a command that does exit(127). If the value of string is NULL, system() returns nonzero if the shell is available, and zero if not. system() does not affect the wait status of any other children. CONFORMING TO
ANSI C, POSIX.2, BSD 4.3 NOTES
As mentioned, system() ignores SIGINT and SIGQUIT. This may make programs that call it from a loop uninterruptable, unless they take care themselves to check the exit status of the child. E.g. while(something) { int ret = system("foo"); if (WIFSIGNALED(ret) && (WTERMSIG(ret) == SIGINT || WTERMSIG(ret) == SIGQUIT)) break; } Do not use system() from a program with suid or sgid privileges, because strange values for some environment variables might be used to subvert system integrity. Use the exec(3) family of functions instead, but not execlp(3) or execvp(3). system() will not, in fact, work properly from programs with suid or sgid privileges on systems on which /bin/sh is bash version 2, since bash 2 drops privileges on startup. (Debian uses a modified bash which does not do this when invoked as sh.) The check for the availability of /bin/sh is not actually performed; it is always assumed to be available. ISO C specifies the check, but POSIX.2 specifies that the return shall always be non-zero, since a system without the shell is not conforming, and it is this that is implemented. It is possible for the shell command to return 127, so that code is not a sure indication that the execve() call failed. SEE ALSO
sh(1), signal(2), wait(2), exec(3) 2001-09-23 SYSTEM(3)
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