I apologize for guessing wrong at what combining.executable does. I made the unwarranted assumption that a file named infile1 would be your 1st input file and that a file named infile2 would be your second input file instead of infile1 being the name of your 2nd input file and infile2 being the name of your 1st input file.
With that list of files and no indication of what produced it, I'll make another wild assumption that the list is the first couple of lines of output from the command:
Code:
ls *header
and that the intent is that your input files are to be processed in increasing alphanumeric sorted order. Assuming that is correct (which based on the failure of my earlier assumptions is certainly not guaranteed), the following will combine your input files and produce an output file named outfile. It uses temporary files named 0 and 1 and renames the last used temporary file to be outfile and removes the other temporary file before it exits:
Code:
#!/bin/ksh
i=0
last=0
for file in *header
do case "$i" in
(0) f1=$file
i=1
;;
(1) combining.executable "$file" "$f1" > $((out = last))
i=2
;;
(2) out=$((1 - last))
combining.executable "$file" $last > $out
last=$out
;;
esac
done
mv $out "outfile"
rm -f $((1 - out))
Although written and tested using a Korn shell, this will work with any shell that uses basic Bourne shell syntax and supports POSIX arithmetic substitutions (such as ash, bash, dash, and ksh; but not csh and its derivatives, and not a traditional Bourne shell).
Hi and thank you for your solution.
I will test it out tomorrow on my files.
Many thanks for your kind help!
---------- Post updated at 12:53 AM ---------- Previous update was at 12:33 AM ----------
Hi,
I actually just tried out your script now :-)
The combining.executable complines that the argument 2 is not specified. It creates files 0 and 1, but they are empty.
Your assumption is correct that the files can be taken in increasing alphanumeric sorted order. Your other assumption that the list of files was generated with command ls is also correct.
Many thanks for your help in advance.
---------- Post updated at 02:19 AM ---------- Previous update was at 12:53 AM ----------
p.s. there is also this:
/bin/ksh: bad interpreter: No such file or directory
Hi and thank you for your solution.
I will test it out tomorrow on my files.
Many thanks for your kind help!
---------- Post updated at 12:53 AM ---------- Previous update was at 12:33 AM ----------
Hi,
I actually just tried out your script now :-)
The combining.executable complines that the argument 2 is not specified. It creates files 0 and 1, but they are empty.
Your assumption is correct that the files can be taken in increasing alphanumeric sorted order. Your other assumption that the list of files was generated with command ls is also correct.
Many thanks for your help in advance.
It sounds like you may have removed some of the <space> characters from the script I suggested???
Please show us the output from the command uname -a. We need to know what operating system (including the release number) that you are using?
What shell are you using (including version number)? If you don't know the version number, show us the output from the command:
Code:
shell --version
where shell is the name of the shell you are using.
Then run the command:
Code:
shell -xv script_name > log 2>&1
where shell is the name of your shell and script_name is the name of the file containing my script. Then show us the exact contents of the 1st 40 lines in the file named log (in CODE tags; not ICODE tags) and show us the output from the commands:
Code:
type combining.executable
printf '%s\n' "$PATH"
ls -l 0 1 log outfile
ls -l *header|head -n 20
(also in CODE tags).
----------------
I just saw your PS. If /bin/ksh isn't a valid path on your system, how did you run the script to produce files 0 and 1 and if trying to run my script produced that error, what else did you do that attempted to run combining.executable???
I did not alter your script, just copy pasted it into a shell and run it. When the shell produced an error of /bin/ksh: bad interpreter: No such file or directory, I deleted the first line of your code and tried it that way. Other than that, I didn't change anything.
Here are the answers to your questions:
Question1: Please show us the output from the command uname -a . We need to know what operating system (including the release number) that you are using?
Question 2: What shell are you using (including version number)?
Answer:
Code:
GNU bash, version 4.1.2(1)-release (x86_64-redhat-linux-gnu)
Copyright (C) 2009 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>[/ICODE]
Question 3: show the first 40 lines of output from this command [ICODE]shell -xv script_name > log 2>&1
Answer:
Code:
module () { eval `/usr/bin/modulecmd bash $*`
}
#!/bin/ksh
i=0
+ i=0
last=0
+ last=0
for file in *header
do case "$i" in
(0) f1=$file
i=1
;;
(1) ./match.pl -f "$file" -g "$f1" -k 1 -l 1 -v "5 6 7" > $((out = last))
i=2
;;
(2) out=$((1 - last))
./match.pl -f "$file" -g $last -k 1 -l 1 -v "5 6 7" > $out
last=$out
;;
esac
done
+ for file in '*header'
+ case "$i" in
+ f1=9477885102_R01C01header
+ i=1
+ for file in '*header'
+ case "$i" in
+ ./match.pl -f 9477885102_R01C02header -g 9477885102_R01C01header -k 1 -l 1 -v '5 6 7'
+ i=2
+ for file in '*header'
+ case "$i" in
+ out=1
+ ./match.pl -f 9477885102_R02C01header -g 0 -k 1 -l 1 -v '5 6 7'
Must specify file one using -g switch
+ last=1
+ for file in '*header'
+ case "$i" in
+ out=0
+ ./match.pl -f 9477885102_R02C02header -g 1 -k 1 -l 1 -v '5 6 7'
+ last=0
I'm sorry,but I'm not able to share the answers to the following commands because they would contain sensitive information.
Code:
type combining.executable
printf '%s\n' "$PATH"
ls -l 0 1 log outfile
ls -l *header|head -n 20
Question 4: the output form the following commands:
Please also show us the output from the commands:
Code:
ls -l "$SHELL"
answer:
Code:
-rwxr-xr-x 1 root root 941880 Dec 22 2015 /bin/bash*
-rwxr-xr-x 1 root root 941880 Dec 22 2015 /bin/bash*
Code:
type ksh
answer:
Code:
-bash: type: ksh: not found
In this case do what Don Cragun already (implicitly) suggested in post #8:
change the line in his script where the shell to be used to execute it is named:
Code:
#! /bin/ksh
and replace it with a line pointing to a shell valid on your system, namely (from your quoted output above)
Code:
#! /bin/bash
Further, to spare you one source of common problems with this line (which is, informally, also called a "shebang"): the line needs to be the very first line in the file and it must not be indented! Even a leading space would make it a normal comment (instead of this special one which tells the OS which shell executable to use to have it interpreted) without any further meaning.
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