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Full Discussion: Redirecting stdout inside a loop
Top Forums UNIX for Dummies Questions & Answers Redirecting stdout inside a loop Post 302912755 by Corona688 on Monday 11th of August 2014 05:22:41 PM
Old 08-11-2014
Quote:
Originally Posted by hmortens
is it possible to organize it real time? like as it is being written to file?
That's your program's output. Once it's written to the file, it's too late to do anything about it inside the loop. Organize it before you put it into the file.


Quote:
I was not specific about this before because I thought it would be the same pattern search, but I need to pull lines containing "No. input reads:", "No. reads in analysis:", "mapped...reads to genomes(s)", and "Detected:"
If you want to pile all three commands together then filter them, do it like this, before it gets to the file:

Code:
for ... in ...
do
        # All commands get piped through egrep, which then prints to stdout
        (
                command1
                command2
                command3
        ) | egrep 'expression1|expression2|expression3'

        # This file gets printed to stdout
        cat restoffile

# Everything printed to stdout gets saved to onesingleoutputfile, in order
done > onesingleoutputfile

The ( ) join them together in a subshell, letting you put a pipe on the end to filter the contents of all three.
Last edited by Corona688; 08-11-2014 at 06:54 PM..
 

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LEARN ABOUT X11R4

zipgrep

ZIPGREP(1)						      General Commands Manual							ZIPGREP(1)

NAME

       zipgrep - search files in a ZIP archive for lines matching a pattern

SYNOPSIS

       zipgrep [egrep_options] pattern file[.zip] [file(s) ...]  [-x xfile(s) ...]

DESCRIPTION

       zipgrep	will  search  files  within  a ZIP archive for lines matching the given string or pattern.  zipgrep is a shell script and requires
       egrep(1) and unzip(1) to function.  Its output is identical to that of egrep(1).

ARGUMENTS

       pattern
	      The pattern to be located within a ZIP archive.  Any string or regular expression accepted by egrep(1) may be used.  file[.zip] Path
	      of  the  ZIP archive.  (Wildcard expressions for the ZIP archive name are not supported.)  If the literal filename is not found, the
	      suffix .zip is appended.	Note that self-extracting ZIP files are supported, as with any other ZIP archive; just	specify  the  .exe
	      suffix (if any) explicitly.

       [file(s)]
	      An  optional list of archive members to be processed, separated by spaces.  If no member files are specified, all members of the ZIP
	      archive are searched.  Regular expressions (wildcards) may be used to match multiple members:

	      *      matches a sequence of 0 or more characters

	      ?      matches exactly 1 character

	      [...]  matches any single character found inside the brackets; ranges are specified by a beginning character, a hyphen, and an  end-
		     ing character.  If an exclamation point or a caret (`!' or `^') follows the left bracket, then the range of characters within
		     the brackets is complemented (that is, anything except the characters inside the brackets is considered a match).

	      (Be sure to quote any character that might otherwise be interpreted or modified by the operating system.)

       [-x xfile(s)]
	      An optional list of archive members to be excluded from processing.  Since wildcard characters  match  directory	separators  (`/'),
	      this  option  may  be used to exclude any files that are in subdirectories.  For example, ``zipgrep grumpy foo *.[ch] -x */*'' would
	      search for the string ``grumpy'' in all C source files in the main directory of the ``foo'' archive, but none in any subdirectories.
	      Without the -x option, all C source files in all directories within the zipfile would be searched.

OPTIONS

       All options prior to the ZIP archive filename are passed to egrep(1).

SEE ALSO

       egrep(1), unzip(1), zip(1), funzip(1), zipcloak(1), zipinfo(1), zipnote(1), zipsplit(1)

URL

       The Info-ZIP home page is currently at
       http://www.info-zip.org/pub/infozip/
       or
       ftp://ftp.info-zip.org/pub/infozip/ .

AUTHORS

       zipgrep was written by Jean-loup Gailly.

Info-ZIP							   20 April 2009							ZIPGREP(1)
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