Renaming files using list

Try this:

for f in *.txt; do d="$(head -1 "$f" | awk '{print $1}').txt"; if [ ! -f "$d" ]; then mv "$f" "$d"; else echo "File '$d' already exists! Skiped '$f'"; fi; done

or more long variant (as script):

#!/bin/sh
for f in *.txt; do
    d="$(head -1 "$f" | awk '{print $1}').txt"
    if [ ! -f "$d" ]; then
        mv "$f" "$d"
    else
        echo "File '$d' already exists! Skiped '$f'"
    fi
done

In case when destination file exists this one-liner skips it.

With perl's rename :

rename 's/(PMC|\.pdf)//g' *pdf.txt 

Demo :

$ ls *txt
PMC21375.pdf.txt
$ rename -n 's/(PMC|\.pdf)//g' *txt 
PMC21375.pdf.txt -> 21375.txt

from the shell prompt. It's very useful, you can put some perl code like I does in a substitution.

You can remove the -n (dry-run mode switch) when your tests become valids.

There are other tools with the same name which may or may not be able to do this, so be careful.

If you run the following command (linux)

$ file $(readlink -f $(type -p rename))

and you have a result like

.../rename: Perl script, ASCII text executable

then this seems to be the right tool =)

If not, to make it the default (usually already the case) on Debian and derivative like Ubuntu :

$ sudo update-alternatives --set rename /path/to/rename

(replace /path/to/rename to the path of your perl's rename command.

Last but not least, this tool was originally written by Larry Wall, the Perl's dad.