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Top Forums Shell Programming and Scripting Naming output files based on variable parameters and input filenames Post 302931323 by bdeads on Monday 12th of January 2015 01:14:53 PM
Old 01-12-2015
Naming output files based on variable parameters and input filenames

Hello, I have a series of files in sub-directories that I want to loop through, process and name according to the input filename and the various parameters I'm using to process the files. I have a number of each, for example file names like AG005574, AG004788, AG003854 and parameter values like ATd, PZa, RTK1, so I want to end with files like AG005574_ATd, AG005574_PZa, AG005574_RTK1, AG004788_ATd, etc.
I loop through the subfolders, run the process and output the results like so:
Code:
#!/usr/bin/bash
model=1
output=$file
for file in $(find /path/to/files/AG00*/*/ -type f -name 'AG00*.fa');
 do process --out=$output."tab" <options> $file ;
      echo $file
done

Obviously, this names the file by process only, not by process_input, and it only writes one file (the last processed) because it over-writes the others. In the case above, the --out= seems to me to be the key to change to get what I want, but $output$file and variations don't work.
I'm sure this is not a tricky problem but I haven't been able to find or piece together a solution. Any help/tutoring is much appreciated.

Moderator's Comments:
Mod Comment select text first before clicking code button

Last edited by Scrutinizer; 01-12-2015 at 02:40 PM.. Reason: repaired code tags
 

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SH(1)							      General Commands Manual							     SH(1)

NAME
sh, ., break, case, cd, continue, eval, exec, exit, export, for, if, read, readonly, set, shift, trap, umask, wait, while - shell SYNOPSIS
sh [-eiknqstvxu] [-c str] [file] OPTIONS
-c Execute the commands in str -e Quit on error -i Interactive mode; ignore QUIT, TERMINATE, INTERRUPT -k Look for name=value everywhere on command line -n Do not execute commands -q Change qflag from sig_ign to sig_del -s Read commands from standard input -t Exit after reading and executing one command -v Echo input lines as they are read -x Trace -u Unset variables EXAMPLES
sh script # Run a shell script DESCRIPTION
Sh is the shell, which forms the user's main interface with the system. On startup, the shell reads /etc/profile and $HOME/.profile, if they exist, and executes any commands they contain. The Minix shell has most of the features of the V7 (Bourne) shell, including redirect- ion of input and output, pipes, magic characters, background processes, and shell scripts. A brief summary follows, but whole books have been written on shell programming alone. Some of the more common notations are: date # Regular command sort <file # Redirect stdin (standard input) sort <file1 >file2 # Redirect stdin and stdout cc file.c 2>error # Redirect stderr a.out >f 2>&1 # Combine standard output and standard error sort <file1 >>file2 #Append output to file2 sort <file1 >file2 & #Background job (ls -l; a.out) & # Run two background commands sequentially sort <file | wc # Two-process pipeline sort <f | uniq | wc # Three-process pipeline ls -l *.c # List all files ending in .c ls -l [a-c]* # List all files beginning with a, b, or c ls -l ? # List all one-character file names ls ? # List the file whose name is question mark ls '???' # List the file whose name is three question marks v=/usr/ast # Set shell variable v ls -l $v # Use shell variable v PS1='Hi! ' # Change the primary prompt to Hi! PS2='More: ' # Change the secondary prompt to More: ls -l $HOME # List the home directory echo $PATH # Echo the search path echo $? # Echo exit status of previous command in decimal echo $$ # Echo shell's pid in decimal echo $! # Echo PID of last background process echo $# # Echo number of parameters (shell script) echo $2 # Echo second parameter (shell script) echo "$2" # Echo second parameter without expanding spaces echo $* # Echo all parameters (shell script) echo $@ # Echo all parameters (shell script) echo "$@" # Echo all parameters without expanding spaces The shell uses the following variables for specific purposes: SHELL the path of the current shell HOME the default value for the cd(1) command PATH the directories to be searched to find commands IFS the internal field separators for command strings PS1 the primary shell prompt PS2 the secondary shell prompt There are various forms of substitution on the shell command line: `...` Command string between back-quotes is replaced by its output "..." Permits variable substitution between quotes '...' Inhibits variable substitution between quotes $VAR Replaced by contents of variable VAR ${VAR} Delimits variable VAR from any following string The expressions below depend on whether or not VAR has ever been set. If VAR has been set, they give: ${VAR-str} Replace expression by VAR, else by str ${VAR=str} Replace expression by VAR, else by str and set VAR to str ${VAR?str} Replace expression by VAR, else print str and exit shell ${VAR+str} Replace expression by str, else by null string If a colon is placed after VAR, the expressions depend on whether or not VAR is currently set and non-null. The shell has a number of built-in commands: : return true status . fn execute shell script fn on current path break [n] break from a for, until or while loop; exit n levels continue [n] continue a for, until or while loop; resume nth loop cd [dir] change current working directory; move to $HOME eval cmd rescan cmd, performing substitutions eval rescan the current command line exec cmd execute cmd without creating a new process exec <|> with no command name, modify shell I/O exit [n] exit a shell program, with exit value n export [var] export var to shell's children; list exported variables pwd print the name of the current working directory read var read a line from stdin and assign to var readonly [var] make var readonly; list readonly variables set -f set shell flag (+f unsets flag) set str set positional parameter to str set show the current shell variables shift reassign positional parameters (except ${0}) one left times print accumulated user and system times for processes trap arg sigs trap signals sigs and run arg on receipt trap list trapped signals umask [n] set the user file creation mask; show the current umask wait [n] wait for process pid n; wait for all processes The shell also contains a programming language, which has the following operators and flow control statements: # Comment The rest of the line is ignored = Assignment Set a shell variable && Logical AND Execute second command only if first succeeds || Logical OR Execute second command only if first fails (...) Group Execute enclosed commands before continuing for For loop (for ... in ... do ... done) case Case statement ((case ... ) ... ;; ... esac) esac Case statement end while While loop (while ... do ... done) do Do/For/While loop start (do ... until ...) done For/While loop end if Conditional statement (if ... else ... elif ... fi) in For loop selection then Conditional statement start else Conditional statement alternative elif Conditional statement end until Do loop end fi Conditional statement end SEE ALSO
echo(1), expr(1), pwd(1), true(1). SH(1)
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