Shell Programming and Scripting

I have three different linux command scripts that I run for 20+ files in one directory.

it goes like this
FIRST SCRIPT:
grep 'something' -w file > newfile1
.
.
.
grep 'something -w file > newfile20

then I take all these 'newfileN' and run this:
awk 'BEGIN { format="%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" } { printf(format,$1,$15,$4,$4,$4,$4,$2,$3,$4,$4)}' newfile1 > new.newfile1
.
.
.
awk 'BEGIN { format="%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" } { printf(format,$1,$15,$4,$4,$4,$4,$2,$3,$4,$4)}' newfile20 > new.newfile20

then finally I take these 'new.newfileN' and do this:
sed -e 's/[+-]/U0/2' -e 's/[+-]/0/2' -e 's/[+-]/0/2' -e 's/[+-]/0/2' -e 's/+/F/1' -e 's/-/R/2' -e 's/[+-]/../2' -e 's/chr//1' new.newfile1 > new.new.newfile1
.
.
.
sed -e 's/[+-]/U0/2' -e 's/[+-]/0/2' -e 's/[+-]/0/2' -e 's/[+-]/0/2' -e 's/+/F/1' -e 's/-/R/2' -e 's/[+-]/../2' -e 's/chr//1' new.newfile20 > new.new.newfile20


So, is there a way I can make this all into one script so instead of copying and pasting each scripted line 20+ times.

thanks

Try this perhaps (untested):

Code:

for f in $(seq -f file%g 1 20)
do
    grep 'something' -w $f > new$f
    awk -v OFS='\t' '{ print $1,$15,$4,$4,$4,$4,$2,$3,$4,$4 }' new$f > new.new$f
    sed -e 's/[+-]/U0/2' -e 's/[+-]/0/2' -e 's/[+-]/0/2' -e 's/[+-]/0/2' -e 's/+/F/1' -e 's/-/R/2' -e 's/[+-]/../2' -e 's/chr//1' new.new$f > new.new.new$f
done

If you don't need all of the temporary files in between:

Code:

for f in $(seq -f file%g 1 20)
do
    grep 'something' -w $f |
    awk -v OFS='\t' '{ print $1,$15,$4,$4,$4,$4,$2,$3,$4,$4 }' |
    sed -e 's/[+-]/U0/2' -e 's/[+-]/0/2' -e 's/[+-]/0/2' -e 's/[+-]/0/2' -e 's/+/F/1' -e 's/-/R/2' -e 's/[+-]/../2' -e 's/chr//1' > new.$f
done

Thank you, I haven't tried but I have question before I do. Sorry if this is an obvious question, but how do I execute this? Do I copy it into a file and then call it from the command line?

Okay, I think I figured that out. i created a file.sh (with the proper heading and chmod it to 755), then ran it
> sh file.sh

then I got a return error

seq: command not found

looks like my mac doesn't have seq. can i use jot? if so, how would i set it up?

thanks a bunch!

Why did you say "linux command scripts" if you are using a Mac??

Change the first line to for f in file1 file2 file3 ... up to file20 and it should work. Or else use a counter...

You shouldn't need to run it with sh. Once you have made it executable, either use ./file.sh (if you are in the same directory), or use the full path, e.g. /some/directory/file.sh.

Sorry about the confusion. I'm still trying to get a handle on all this. I'm connected to my mac at work via ssh (using my PC from home).

I did what you suggested and it worked like a charm.

but is there a way to forgo writing 20 file names in the first line and instead call them all like you initially had it?