to work. You are aware that -v"REP=<something>" is a declaration of a variable, aren't you? It declares "REP" to hold a certain value inside awk. Would you expect "$x" here:
Code:
x="ls"
to hold a directory listing or rather the string "ls", hmm?
/PS: Is there any reason why you introduce an element "NULL" in every array which you do not use at all?
Code:
...
TMPArray1=( "GGGGGG|TTTTT" "AAAAAA|CCCCCC" "CCAAAA|CCCCAA" )
...
for y in {0..2}
Lets put aside the business with awk and the eval for a moment. ${TMPArray[$y][$e]} is supposed to be a two-dimensional array, a matrix, yes? The two variables "$y" and "$e" should hold row and column, correct?
Now look again at how you defined your arrays: this is not one two-dimensional array (like the one i sketched out for your above, in ksh), but its three one-dimensional arrays which just happen to have similar names.
Let us simplify our requirements for a moment. Instead of using complex parameter-passing calls to awk we simply want to print the content of the arrays using a nested loop to generate the indexes. We also simplify the contents of the arrays:
Now let us construct the outer loop. This one should generate the names of the arrays:
Code:
arr1=( "11" "12" "13" )
arr2=( "21" "22" "23" )
arr3=( "31" "32" "33" )
for row in {1..3} ; do
echo "arr"${row}
done
You are still with me? Good, now for the second, inner loop to count the colums. Notice that array elements are numbered starting with 0, not 1, therefore we let the for-loop run from 0-2, not 1-3. This way we do not need a NULL element which we would ignore.
Code:
arr1=( "11" "12" "13" )
arr2=( "21" "22" "23" )
arr3=( "31" "32" "33" )
for row in {1..3} ; do
echo "arr"${row}
done
Code:
arr1=( "11" "12" "13" )
arr2=( "21" "22" "23" )
arr3=( "31" "32" "33" )
for row in {1..3} ; do
for column in {0..2} ; do
echo "arr"${row}"[$column]"
done
done
Notice that this outputs the names of the variables correctly. But we do not want the names, we want the contents. This is why we restart the process of substituting a variables name with its content a second time. We put an "eval" in front of the command and a (protected by a "\") "$"
Code:
arr1=( "11" "12" "13" )
arr2=( "21" "22" "23" )
arr3=( "31" "32" "33" )
for row in {1..3} ; do
for column in {0..2} ; do
eval echo "\${arr${row}[$column]}"
done
done
The only thing left to explain is why the "$" had to be protected: well, picture how the process of substituting variables names with their contents happens:
Code:
eval echo "\${arr${row}[$column]}" # original line
echo $arr1{[0]} # after one processing
echo 11 # after the second processing
The "$" had to be protected so that it would not be translated in the first processing pass.
Finally! I have to keep the NULL statement to facilitate the handling of the input files
Code:
#!/bin/bash
TMPArray1=( NULL "GGGGGG|TTTTT" "AAAAAA|CCCCCC" "CCAAAA|CCCCAA" )
TMPArray2=( NULL "XXXXX|YYYYYY" "ZZZZZZZ|BBBBBBB" "KKKKKK|LLLLLL" )
TMPArray3=( NULL "SSSSS|FFFFFF" "EEEEEE|JJJJJJ" "PPPPPP|UUUUUU" )
for y in {1..3}
do
for x in {1..3}
do
eval echo "\${TMPArray${y}[$x]}" > tmp | awk -v "REP=$(awk '{print}' tmp)" '{gsub("^.*" REP ".*$","",$0)} 1' $y.$x > $y.Result$x
done
rm tmp
done
It still looks horrible but much better than before and working. Anyway to simplify the awk script? If possible, I would like to avoid the 'tmp' file
Thanks!
Programming (writing a script, however small, IS programming) is a complex activity and you need to do it right, the same way you need to establish a protocol.
When establishing a certain method - say, i want to use a Taqman PCR to establish the expression of a certain protein - we need to not only get one good try but we need to work on the method as long as it takes to get good tries reliably. To show that one certain mouse had a higher expression level means nothing - we would need to show that all the knock-down specimen have significantly higher/lower expression levels than the control group, yes? When writing programs you do not stop once it did once what you want but you work until it does what you want even under the most adverse conditions (or nothing at all, but definitely not doing something you do NOT want), you work until you can understand it well and until a certain "elegance" in the way it is written is reached. *)
Quote:
Originally Posted by Xterra
It still looks horrible but much better than before and working. Anyway to simplify the awk script? If possible, I would like to avoid the 'tmp' file
You are right, it looks ugly - or, as i prefer to say, rather "unelegant". The usage of a (completely unnecessary) "tmp"-file is one of the reasons. But let us start at a basic topic:
Code:
for y in {1..3}
do
for x in {1..3}
Of course for the system it doesn't matter what variable names you use, but YOU - the human reader trying to understand what the program does - it matters big time. Do yourself a favour and give variables a meaningful name: "row" and "column" is more easily understood than "x" and "y". It will not matter how you name variables, but do so in a way you yourself can easily understand its purpose and it possible contents from the name.
Quote:
Originally Posted by Xterra
I have to keep the NULL statement to facilitate the handling of the input files
No! Programming is about keeping order and you should NEVER use such devices. If you want a list of replacements then create a list of replacements, not a list of anything with replacements interspersed. if you need a separate name for a file then create it using a separate variable - there is no shortage of them, for example:
Code:
for outerloop in {1..3} ; do
for innerloop in {0..2} ; do
(( filenamepart = innerloop + 1 ))
eval command \${array${outerloop}[$innerloop]} > file.${filenamepart}.${outerloop}
done
done
At last, let us talk about the intermediate "tmp" file:
First, the pipe is not necessary at all and most probably keeping the line from doing what you want to do. Picture a process (any process - "awk" or any other program) like a garden hose: you pour data into it at the top, and some (processed) data flows out at the bottom. A pipe, to carry on with this picture, means to connect two such garden hoses so that the outflow of one pours into the other.
Some programs take their data from either this input ("stdin") or from files and "awk" is among them. So the following two lines do the same:
Code:
awk '....' inputfile
cat inputfile | awk '...'
"cat" just takes an input file (or "stdin") and spews out what is there. Notice that the following - though not making very much sense - is also doing the same:
Code:
cat inputfile | cat | awk '...'
the first "cat reads from a file and puts its contents to "stdout", which is connected to the "stdin" of the second "cat". This again puts everything going in there to its own "stdout" (we are now through two hoses of the same type) and finally this is connected to "stdin" of awk.
To come back to your line: there is nothing you want to pass through this mechanism to "awk" and therefore this is just redundant. Its just two commands:
Now, when you look closely at the first command, what does go into this file "tmp"? In fact, after all the "eval"s and expansions, it is a certain array element, say "GGGGGG|TTTTT". So, effectively you have there a line that says:
Code:
echo "GGGGGG|TTTTT" > tmp
(yes, the values differ for each execution of the loop, but the schema stays the same). You could - if you don't want to convolute your "awk" statement too much, which is a good idea, always do one thing in a step, but do it good - put it in a variable:
bakunin
__________________
*) this is a difficult topic to explain to a novice and you will probably just have to believe me - at least for the moment. I can tell you that "elegantly written" programs tend to work better and are more easily maintained than "unelegant" ones.
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