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Full Discussion: [Solved] Running a R script with in a shell script
Top Forums Shell Programming and Scripting [Solved] Running a R script with in a shell script Post 302886310 by Kanja on Thursday 30th of January 2014 02:51:39 PM
Old 01-30-2014
[Solved] Running a R script with in a shell script
Hi,

I do have an R script named KO.R. Basically reads thousands of files, whose name has a pattern that differs at a portion of the file name, List.txt.

Row_file1_mile.txt
Row_file2_mile.txt
Row_file3_mile.txt
...
...
Row_file1000_mile.txt

Below is a portion of my Rscript that reads the file.
Code:
vi KO.R

Sample =
  read.delim("/Users/dropBox/Row_$file_mile.txt")
...
...
...

If I provide the list of the variable portion of the file name like

Code:
file1
file2
file3
...
..
file1000

how could I run this script one by one by reading each of the files and execute the script.

This is what I tried by making a .sh file
Code:
while read file
do

R CMD BATCH KO.R 

done < /Users/dropBox/List.txt

where List.txt contains the list of the variable portion of the file.

Could you please let me know the best way to excecute this R script with in the .sh executable shell script?
 

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LEARN ABOUT DEBIAN

trcs

trcs(1) 							   User Manuals 							   trcs(1)

NAME

       trcs - convert text files from one codeset to other

SYNOPSIS

       trcs -C | -l | -h

       trcs [-s] [-f input-codeset ] [-t output-codeset ] [ file ]...

DESCRIPTION

       trcs  is a program for translation of text files from one codeset to other.  When exact translation is impossible it tries to make approxi-
       mations.  For example pseudographic characters are approximated by ASCII characters in codesets that have no pseudographic  characters  and
       characters with diacritical marks are approximated by existing characters.

       If the option -s or --gen-script is given trcs will generate simple script that invokes tr(1) This is useful if you want to include this in
       your script or for faster conversion of many files.

       If none of -C, -s, -l, -h and their equivalents is given each file will be read assuming it is coded with codeset input-codeset On standard
       output  it will be recoded so to use codeset output-codeset If there is no file given trcs will act as filter.  Both input-codeset and out-
       put-codeset are case insensitive and default to `cp1251'.

OPTIONS

       -C, --copyright
	      Display copying conditions and warranty information.

       -s, --gen-script
	      Generates conversion script for given input and output encodings instead to convert text files.

       -l, --list
	      List all known codesets with their aliases.

       -h, --help
	      Display this help and exit.

       -f input-codeset, --from[=]input-codeset
	      Codeset of the source.

       -f output-codeset, --to[=]output-codeset
	      Codeset of the output.

EXAMPLES

       trcs -fcyrillic -t koi8-r letter.txt
	      Convert letter.txt from ISO-8859-5 (cyrillic) to KOI8-R and output the result on standard output.

       trcs --from cp437 --to=mik --gen-script >ibm2mik
	      Generates script ibm2mik for converting from CP437 to MIK.

       sh ibm2mik screen.txt
	      Convert screen.txt from CP437 to MIK.  Output the result on standard output.  Without parameters ibm2mik acts as filter.

AUTHOR

       Anton Zinoviev <anton@lml.bas.bg>, <zinoviev@fmi.uni-sofia.bg>

SEE ALSO

       tr(1)

Linux								     JUN 2000								   trcs(1)
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