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Top Forums Shell Programming and Scripting Copy of array by index value fails Post 303012768 by RudiC on Thursday 8th of February 2018 04:36:04 PM
Old 02-08-2018
Now this is a problem spec difficult to understand, and I'm not sure I did. Nevertheless, this "proof of concept" worked on a two record file created from your sample. It requires a recent bash (don't run with your above shebang!), and it assumes replacements in every record. Should that not be the case, additional logics is required. The cats are NOT "uuoc"s but are needed for line numbering for later sorting. Be careful with the distinction between <TAB>s and spaces! Give it a try and come back with results...

Code:
prefix=015_
name_tag=CompoundName
sub_tag=Identifier
mapfile < <(cat -n input_file | grep -A1 "^ *1	\|$name_tag\|$sub_tag\|\$\$\$\$" | grep -v "$name_tag\|$sub_tag\|\$\$\$\$\|--\|^ *2	") REP
for ((i=0; i<${#REP[@]}; i+=3))
  do	REP[i+1]="${REP[i+1]%%	*}	PubChem_CID_${REP[i+2]#*	}"
	REP[i]="${REP[i]%%	*}	${prefix}${REP[i+1]#*	}"
	unset REP[i+2]
  done
PAT=${REP[@]%%	*}
PAT="^ *\(${PAT// /\\|}\)	"
sort -k1,1n  <(echo "${REP[@]}") <(cat -n input_file | grep -v "$PAT") | cut -f2-


Last edited by RudiC; 02-08-2018 at 05:42 PM..
This User Gave Thanks to RudiC For This Post:
 

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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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