1

Normally, looping over the files I use basename to extract the name of the file as a separate variable:

# remove .pdb extension from filename in new variable and print name of the file without it
for pdb in "${storage}"/complex*.pdb ; do
pdb_name=$(basename "$pdb" .pdb)
echo this is "$pdb_name" without its extension!
done

How could I remove several patterns from each file using the same basename expression? For instance, in addition to ".pdb" I would like to omit also "complex", which is always present at the beginning of each file (here I used it as a pattern to recognize file in for LOOP).

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1 Answer 1

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3

As far as I know, basename can not remove a prefix from the non-directory portion of a path. I would suggest using parameter expansion features instead:

shopt -s nullglob   # Don't loop over the pattern if it matches nothing
for pdb in "$storage"/complex*.pdb
do
  pdb_name=${pdb##*/complex}
  pdb_name=${pdb_name%.pdb}
  printf '%s\n' "$pdb_name"
done

${pdb##*/complex} expands to the value of pdb with the longest prefix that matches the */complex shell pattern removed.

${pdb_name%.pdb} expands to the value of pdb_name with the shortest suffix matching the .pdb shell pattern removed.

While this is not an issue in your case, note that base_name=$(basename "$path") strips newline characters at the end of file names (because of command substitution) as a likely unwanted side effect. Shell parameter expansion is safer in this respect.

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  • thank you! as I understood correclt it is not possible to do those two editions in one basename command, isn't it ? Commented Oct 21, 2020 at 9:53
  • As far as I know, no, basename can't remove a prefix from the last component of a path. Commented Oct 21, 2020 at 9:58

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