LinuxQuestions.org - [SOLVED] Generating two bash arguments from 'ls'

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Generating two bash arguments from 'ls'

Dear Forum
Say I have a directory containing the following files.

Code:

1-res-opt-I189N-0001.pdb

1-res-opt-I189N-0002.pdb

1-res-opt-I189N-0003.pdb

1-res-opt-I189N-0004.pdb

1-res-opt-I189N-0005.pdb

1-res-opt-I189N-0006.pdb

1-res-opt-I189N-0007.pdb

1-res-opt-I189N-0008.pdb

1-res-opt-I189N-0009.pdb

1-res-opt-I189N-0010.pdb

3-res-opt-I189N-0001.pdb

3-res-opt-I189N-0002.pdb

3-res-opt-I189N-0003.pdb

3-res-opt-I189N-0004.pdb

3-res-opt-I189N-0005.pdb

3-res-opt-I189N-0006.pdb

3-res-opt-I189N-0007.pdb

3-res-opt-I189N-0008.pdb

3-res-opt-I189N-0009.pdb

3-res-opt-I189N-0010.pdb

What I want is something like:

Code:

for i in *.pdb

do

python my_script.py 1-res-opt-I189N-00{1..10}.pdb 3-res-opt-I189N-00{1..10}.pdb

done

such that always the two files with corresponding index are submitted together to the Python script.
How do I do that?
Thanks for any hints.

If you have bash 4 you can use extended brace expansion with zero-padded numbers:

Code:

for i in {0001..10}

do

  python my_script.py 1-res-opt-I189N-$i.pdb 3-res-opt-I189N-$i.pdb

done

Otherwise use printf and command substitution:

Code:

for i in {1..10}

do

  python my_script.py 1-res-opt-I189N-$(printf "%04d" $i).pdb 3-res-opt-I189N-$(printf "%04d" $i).pdb

done

In any case the iteration variable of the loop should be a number, not the whole filename. Hope this helps.

more than helpful. Thanks.

For the record, this is what your original code does...

Code:

for i in *.pdb

do

python my_script.py 1-res-opt-I189N-00{1..10}.pdb 3-res-opt-I189N-00{1..10}.pdb

done

"for i in *.pdb" first sets the variable "i" to each individual filename in the directory in turn. But then it's never used anywhere.

Inside the loop you have a line with brace expansions inserted. These get expanded before execution, so you get a single command that looks like this:

Code:

python my_script.py 1-res-opt-I189N-001.pdb 1-res-opt-I189N-002.pdb 1-res-opt-I189N-003.pdb 1-res-opt-I189N-004.pdb 1-res-opt-I189N-005.pdb 1-res-opt-I189N-006.pdb 1-res-opt-I189N-007.pdb 1-res-opt-I189N-008.pdb 1-res-opt-I189N-009.pdb 1-res-opt-I189N-0010.pdb 3-res-opt-I189N-001.pdb 3-res-opt-I189N-002.pdb 3-res-opt-I189N-003.pdb 3-res-opt-I189N-004.pdb 3-res-opt-I189N-005.pdb 3-res-opt-I189N-006.pdb 3-res-opt-I189N-007.pdb 3-res-opt-I189N-008.pdb 3-res-opt-I189N-009.pdb 3-res-opt-I189N-0010.pdb

...which you then execute over and over again, once for each file in the directory.

As colucix demonstrated, generate the list of files you want to use (or in this case a sequence of numbers that can be used inside the loop to match filenames) first, then feed that to the for loop and use the variable set by it to access them one at a time.

By the way, for zero padding in bash 3, you could also simply do something like this:

Code:

for i in 000{1..9} 0010 ; do

See here for more on how to do zero padding:
http://mywiki.wooledge.org/BashFAQ/018

@david the h.:
thanks a lot. very informative post.
kind regards