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Top Forums UNIX for Dummies Questions & Answers Redirecting stdout inside a loop Post 302912731 by Corona688 on Monday 11th of August 2014 02:51:21 PM
Old 08-11-2014
Now we're getting somewhere.

Let me change your pseudocode a little bit. Do you really mean:

Code:
for VAR in "$LOCATION"/*_fastqc/summary.txt
do
        cat "$VAR"
        print /Processed reads/ for that sample (which comes from where exactly?  You have given no input so we cannot tell.)
        print /Trimmed reads/ for that sample (which comes from what exactly?  You have given no input so we cannot tell.)
done > combined.txt

 

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cat(1)							      General Commands Manual							    cat(1)

Name
       cat - concatenate and print data

Syntax
       cat [ -b ] [ -e ] [ -n ] [ -s ] [ -t ] [ -u ] [ -v ] file...

Description
       The  command reads each file in sequence and displays it on the standard output.  Therefore, to display the file on the standard output you
       type:
       cat file
       To concatenate two files and place the result on the third you type:
       cat file1 file2 > file3
       To concatenate two files and append them to a third you type:
       cat file1 file2 >> file3
       If no input file is given, or if a minus sign (-) is encountered as an argument, reads from the standard input file.  Output is buffered in
       1024-byte blocks unless the standard output is a terminal, in which case it is line buffered.  The utility supports the processing of 8-bit
       characters.

Options
       -b   Ignores blank lines and precedes each output line with its line number.

       -e   Displays a dollar sign ($) at the end of each output line.

       -n   Precedes all output lines (including blank lines) with line numbers.

       -s   Squeezes adjacent blank lines from output and single spaces output.

       -t   Displays non-printing characters (including tabs) in output.  In addition to those representations used with the -v  option,  all  tab
	    characters are displayed as ^I.

       -u   Unbuffers output.

       -v   Displays  non-printing  characters (excluding tabs and newline) as the ^x.	If the character is in the range octal 0177 to octal 0241,
	    it is displayed as M-x. The delete character (octal 0177) displays as ^?.  For example, is displayed as ^X.

See Also
       cp(1), ex(1), more(1), pr(1), tail(1)

																	    cat(1)
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