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Full Discussion: Optimizing sed command
Top Forums Shell Programming and Scripting Optimizing sed command Post 302238561 by jolecanard on Saturday 20th of September 2008 05:25:56 PM
Old 09-20-2008
Optimizing sed command

Hi,

I would like to know if there is a command faster then sed, or a way to optimize my code...

Here is the description of my problem:
I have a file "file1" that is composed of 10 columns. The first one contain a list of ID, the second a list of number associated to the firs list of ID. The third one contains ID and the fourth the number associated, etc...

So I have:
Code:
ID  numb  ID  numb  ID   numb   ID   numb   ID   numb
ID  numb  ID  numb  ID   numb   ID   numb   ID   numb
...
...

The total number of ID is around 8000.

I want to find all the ID starting by a given string (eg. "460...") and extract the associated number. To do that I am simply using a grep command associated with cut and it is going pretty well.

Then I am doing an operation on the numbers extracted (MATLAB) and then I need to put the new values back in place in the file with 10 columns. To do that I am using:
Code:
x=file1
count=1
for k in $listID
do
  VALUE=`head -$count newval | tail -1`
  sed 's/'$k'  .\.....E.../'$k'  '$VALUE'/g' $x > extps
  \mv extps $x
  count=`expr $count + 1`
done

Where "newval" is the list of the new values computed, "listID" is the list of all the ID for which I need to change the associated number and "file1" is hte file with the 10 columns.

This code is working perfectly, but because I have a bunch of ID to change the repeted use of sed is taking A LOT of time (among 8000 ID I need to change about 500).

Does anybody know how could I speed up this code?

Thanks
 

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SED(1)							      General Commands Manual							    SED(1)

NAME
sed - stream editor SYNOPSIS
sed [ -n ] [ -g ] [ -e script ] [ -f sfile ] [ file ... ] DESCRIPTION
Sed copies the named files (standard input default) to the standard output, edited according to a script of commands. The -f option causes the script to be taken from file sfile; these options accumulate. If there is just one -e option and no -f's, the flag -e may be omitted. The -n option suppresses the default output; -g causes all substitutions to be global, as if suffixed g. A script consists of editing commands, one per line, of the following form: [address [, address] ] function [argument ...] In normal operation sed cyclically copies a line of input into a pattern space (unless there is something left after a command), applies in sequence all commands whose addresses select that pattern space, and at the end of the script copies the pattern space to the standard out- put (except under -n) and deletes the pattern space. An address is either a decimal number that counts input lines cumulatively across files, a that addresses the last line of input, or a con- text address, /regular-expression/, in the style of regexp(6), with the added convention that matches a newline embedded in the pattern space. A command line with no addresses selects every pattern space. A command line with one address selects each pattern space that matches the address. A command line with two addresses selects the inclusive range from the first pattern space that matches the first address through the next pattern space that matches the second. (If the second address is a number less than or equal to the line number first selected, only one line is selected.) Thereafter the process is repeated, looking again for the first address. Editing commands can be applied to non-selected pattern spaces by use of the negation function (below). An argument denoted text consists of one or more lines, all but the last of which end with to hide the newline. Backslashes in text are treated like backslashes in the replacement string of an command, and may be used to protect initial blanks and tabs against the stripping that is done on every script line. An argument denoted rfile or wfile must terminate the command line and must be preceded by exactly one blank. Each wfile is created before processing begins. There can be at most 120 distinct wfile arguments. a text Append. Place text on the output before reading the next input line. b label Branch to the : command bearing the label. If label is empty, branch to the end of the script. c text Change. Delete the pattern space. With 0 or 1 address or at the end of a 2-address range, place text on the output. Start the next cycle. d Delete the pattern space. Start the next cycle. D Delete the initial segment of the pattern space through the first newline. Start the next cycle. g Replace the contents of the pattern space by the contents of the hold space. G Append the contents of the hold space to the pattern space. h Replace the contents of the hold space by the contents of the pattern space. H Append the contents of the pattern space to the hold space. i text Insert. Place text on the standard output. n Copy the pattern space to the standard output. Replace the pattern space with the next line of input. N Append the next line of input to the pattern space with an embedded newline. (The current line number changes.) p Print. Copy the pattern space to the standard output. P Copy the initial segment of the pattern space through the first newline to the standard output. q Quit. Branch to the end of the script. Do not start a new cycle. r rfile Read the contents of rfile. Place them on the output before reading the next input line. s/regular-expression/replacement/flags Substitute the replacement string for instances of the regular-expression in the pattern space. Any character may be used instead of For a fuller description see regexp(6). Flags is zero or more of g Global. Substitute for all non-overlapping instances of the regular expression rather than just the first one. p Print the pattern space if a replacement was made. w wfile Write. Append the pattern space to wfile if a replacement was made. t label Test. Branch to the command bearing the label if any substitutions have been made since the most recent reading of an input line or execution of a If label is empty, branch to the end of the script. w wfile Write. Append the pattern space to wfile. x Exchange the contents of the pattern and hold spaces. y/string1/string2/ Transform. Replace all occurrences of characters in string1 with the corresponding character in string2. The lengths of string1 and string2 must be equal. !function Don't. Apply the function (or group, if function is only to lines not selected by the address(es). : label This command does nothing; it bears a label for b and t commands to branch to. = Place the current line number on the standard output as a line. { Execute the following commands through a matching only when the pattern space is selected. An empty command is ignored. EXAMPLES
sed 10q file Print the first 10 lines of the file. sed '/^$/d' Delete empty lines from standard input. sed 's/UNIX/& system/g' Replace every instance of by sed 's/ *$// drop trailing blanks /^$/d drop empty lines s/ */ replace blanks by newlines /g /^$/d' chapter* Print the files chapter1, chapter2, etc. one word to a line. nroff -ms manuscript | sed ' ${ /^$/p if last line of file is empty, print it } //N if current line is empty, append next line /^ $/D' if two lines are empty, delete the first Delete all but one of each group of empty lines from a formatted manuscript. SOURCE
/sys/src/cmd/sed.c SEE ALSO
ed(1), grep(1), awk(1), lex(1), sam(1), regexp(6) L. E. McMahon, `SED -- A Non-interactive Text Editor', Unix Research System Programmer's Manual, Volume 2. BUGS
If input is from a pipe, buffering may consume characters beyond a line on which a command is executed. SED(1)
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