hey i have a doubt, suppose in the script i include an exe type of file for ex. ./a.out, which takes input as a pdb file namely 1sn3.pdb, now i want my output text file to contain the name 1sn3.txt , how do i do that using the shell script ???
is there any method ???? or any command ???

please let me know

Hi,

Assuming that this is done in bash and there is a variable that holds 1sn3.pdb you can do this:

fullFileName="1sn3.pdb" <-- the varibale I assumed)
namePart=${fullFileName%.*}

namePart now holds everything before the last dot (1sn3 in this case).

Adding a new extension: newFileName="${namePart}.txt"

This could be done in one command: newFileName="${fullFileName%.*}.txt"

Hope this helps.

No thee input file i give while the script is running. So how can i assign variable for that?

Hi,

While running or when starting? Both need a different approach.

For the first one read <var> comes to mind.

The second one can be done in several ways, but script <inputfile> is often used. The name of the inputfile is represented as $1 ($2 being the second option, $3 being the third. I.e: script file1 file2 file3).

Although you can use $1 in all of the script, for readability you transfer it to a "human readable" variable (inputfile="$1") and work with inputfile in the rest of the script.

These questions seem to be hypothetical, if you want a good guide to bash scripting take a look here: Advanced Bash-Scripting Guide.

Hope this helps.

Based on Druuna's comments your bash script would look like this:

fullFileName="1sn3.pdb"
newFileName="${fullFileName%.*}.txt"
./a.out fullFileName > newFileName # assuming that a.out outputs to stdout as plain text output

Your script could also read a file containing a list of .pdb filenames - in that case the above sample would need to go into a loop sequence until all entries are processed.

Somewhat off-topic: this is a question, not a doubt.
http://wordnetweb.princeton.edu/perl/webwn?s=question
http://wordnetweb.princeton.edu/perl/webwn?s=doubt



Cheers,
Tink

hey i meant tat suppose this is my script :

when i run it ./test.sh
it ll ask Enter filename:
then suppose i enter 1d6a.pdb
the output file is given as teta

now i want this teta to have the name as 1d6a

how do i do that ?

Hi,

Here's a simple bash script that does so:

Testrun:

Hope this helps.

Hey u r not getting my exact question. the script includes a exe file which asks for the input file in the command prompt.

like this :when u run ./test.sh it asks, i want the file name ans1 to be written as 1d6a