1

I have a list of files in directory They are named:

2.pdb
3.pdb
14.pdb
...
200.pdb
...
1240.pdb

I'd like to combine all of these in this specific order. When I use

cat *pdb > pdb_all.txt 

it seems it just makes a random combination (or perhaps it starts will all files that begin with the number 1 (no matter if it is 1, 10 or, 1000). Can I make this command combine my files in a specific order, or do I rename all my files to contain 4 digits (e.g. 0002, 0003, 0014 etc). I suspect the latter is the easiest way, but how to I do this with the mv command on a mac?

2
  • You specifically want to use mv (no python)? renaming can be done "virtually", to skip the actual renaming step. – Jacob Vlijm Mar 9 '15 at 11:59
  • I am all new to bash - so it's just because I've tried to use mv before and I sort of understand it. It's nicest to do something that I understand :) – Ditte Mar 9 '15 at 12:08
1

The easiest way is as you say to rename your files and add leading zeroes. You can do this in the terminal on your mac like this:

for a in *.pdb; do mv $a `printf %05d.%s ${a%.*} ${a##*.}`; done

In this example i set that each number should contain 5 digits. So 1.pdb will be renamed to 00001.pdb. However you could lower that to 4 or whatever suits your need.

Good luck!

Edit

To make it work with pdbid.1 suffix, this is the answer:

for a in *.pdbid.1; do mv $a `printf %05d.%s ${a%.*.*} ${a#*.}`; done
9
  • I don't know how it went wrong for me. I ended up with all my files in the directory deleted and replaced by one new file named 0000.pdb... :S – Ditte Mar 9 '15 at 12:07
  • Are you sure you copied the command exactly as I described it ? It tested it just now on a machine runnint yosemite - and it works there. – stalet Mar 9 '15 at 12:11
  • I've just tried it twice again. I've copied-pasted it, and now it gives me a very long text in the terminal saying "-bash: printf: 102.pdbid: invalid number -bash: printf: 1033.pdbid: invalid number -bash: printf: 1035.pdbid: invalid number -bash: printf: 1073.pdbid: invalid number -bash: printf: 1121.pdbid: invalid number (continuing...) and ending with 0000.936.pdbid0000.955.pdbid0000.966.pdbid0000.978.pdbid0001.: No such file or directory. There are no new files in my directory (I exchanged pdb with pdbid.1 'cause that's my extension and changed 5 to 4) – Ditte Mar 9 '15 at 12:16
  • are there more than one punctuation in your filenames ? – stalet Mar 9 '15 at 12:19
  • don't think so. they are all e.g. 2.pdbid.1 and 14.pdbid.1 – Ditte Mar 9 '15 at 12:20
1

I would use a combination of find, sort and xargs to achieve something like this.

find ./ -name "*.pdb" | sort -n | xargs cat > pdb_all.txt

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