Sorry, I didn't see these last two posts, I will give the code a try.
LMHmedchem
---------- Post updated at 03:01 PM ---------- Previous update was at 02:42 PM ----------
Well using the script posted by alister, I get the following error,
line 14: ed: command not found
line 14 is,
printf %s\\n 1c "$f" . w q | ed -s "$f"
If I add the code from agama, I get the following error,
line 5: cd: ./test_script/: No such file or directory
abort: could not switch to './test_script/' or parameter was missing
This is the code I am using,
Code:
#!/usr/bin/bash
# mol_filename2firstline_2.sh
cd "$1"
if ! cd "${1:-no-such-directory}" # also quote on the off chance that something in the path has spaces
then
echo "abort: could not switch to '$1' or parameter was missing"
exit 1
fi
for f in *; do
[ ! -f "$f" ] && continue
if [ -s "$f" ]; then
printf %s\\n 1c "$f" . w q | ed -s "$f"
else
printf %s\\n "$f" > "$f"
fi
done
run as,
./mol_filename2firstline_2.sh test_script/
I did stick my code into the loop to see what would happen, and it does work.
Code:
#!/usr/bin/bash
# mol_filename2firstline_3.sh
# accepts a directly name dir/ and add replaces the first line of all .mol files
# with the filename
cd "$1"
for f in *.mol; do
sed "1 c\\$f" $f > TEMP
cp -f TEMP $f
rm -f TEMP
done
You only need the cd command in the if statement. Your directory is a relative path (doesn't start with a slant) and that is why it's erroring (there isn't a ./xxxx directory inside of the directory which you switched to earlier in the script.
You also are wasting effort copying the file back in your script (extra i/o adds to the latency).
Code:
#!/usr/bin/bash
# mol_filename2firstline_2.sh
### unneeded cd "$1"
if ! cd "${1:-no-such-directory}" # also quote on the off chance that something in the path has spaces
then
echo "abort: could not switch to '$1' or parameter was missing"
exit 1
fi
ls | while read f # for * doesn't handle filenames with spaces or large numbers of files.
do
[ ! -f "$f" ] && continue
printf %s\\n "$f" >"$f.new"
if ! sed '1d' "$f" >>"$f.new"
then
rm "$f.new"
else
mv "$f.new" "$f"
fi
done
What operating system are you using that it doesn't have ed? I'm curious.
I'm running cygwin under windows xp. I know that cygwin has ed, but I may not have the package installed.
I didn't recognize that the cd command was going to execute twice.
Quote:
Originally Posted by agama
You also are wasting effort copying the file back in your script (extra i/o adds to the latency).
I ran you code on a set of 900 files and it takes ~45s, compared to 1m6s for my code, so this works pretty well.
The files I will use this on always have the extension .mol, I added that to my code for some extra security in case there happen to be some other files in the directory. Using your code, I could do ls *.mol | etc, but would that invoke the same issue you were trying to avoid by using ls in the first place (spaces, etc)? I suppose logic could be added to the loop to test if the filename ends in .mol and skip it if not.
Something like,
Code:
#!/usr/bin/bash
# mol_filename2firstline_4.sh
if ! cd "${1:-no-such-directory}" # also quote on the off chance that something in the path has spaces
then
echo "abort: could not switch to '$1' or parameter was missing"
exit 1
fi
ls | while read f # for * doesn't handle filenames with spaces or large numbers of files.
do
[ ! -f "$f" ] && continue
EXTENSION=`echo ${f: -4}`if [ "$EXTENSION" == ".mol" ]; then
printf %s\\n "$f" >"$f.new"
if ! sed '1d' "$f" >>"$f.new"
then
rm "$f.new"
else
mv "$f.new" "$f"
fi
else
echo $f # alert user if files other than .mol were found
fi
done
LMHmedchem
Last edited by LMHmedchem; 06-09-2012 at 05:14 PM..
You are correct, adding the globbing to the ls command would have the same possible consequences as using the glob on the for.
Your solution is on the right track; you don't need the echo to assign the value to EXTENSION, and since you are using bash, you don't even need to create the variable.
Code:
EXTENSION="${f: -4}" # if you prefer to keep the variable, just assign it directly no need for backtics
Code:
ls | while read f # for * doesn't handle filenames with spaces or large numbers of files.
do
[ ! -f "$f" ] && continue
if [[ "$f" == *".mol" ]]; then
printf %s\\n "$f" >"$f.new"
if ! sed '1d' "$f" >>"$f.new"
then
rm "$f.new"
else
mv "$f.new" "$f"
fi
else
echo $f # alert user if files other than .mol were found
fi
Both bash and kshell support pattern matching (don't confuse with regular expression matching) inside of the [[...]] construct. This allows you to test for the contents of f without needing to chop it up.
if ! cd "${1:-no-such-directory}" # also quote on the off chance that something in the path has spaces
then
echo "abort: could not switch to '$1' or parameter was missing"
exit 1
fi
ls | while read f # for * doesn't handle filenames with spaces or large numbers of files.
If you want to ensure that the script has been given a viable working directory, then $1 should be tested to confirm that it's non-empty and a directory. In that instance, blindly substituting a string in that way can be dangerous.
You are mistaken about the for f in * ... construct. Since pathname expansion occurs after field splitting, the expansion of * is absolutely safe with regard to IFS characters (by default, space, tab, and newline).
Ironically, the statement you replaced it with does not handle spaces correctly in all cases. If ls prints a filename with leading or trailing spaces, read will discard those, yielding either a non-existent file or a different file. Further, if the filename ended with a backslash, that backslash would be stripped and the next filename in the list, if any, would be appended. while IFS= read -r f fixes both issues.
Demonstration:
Code:
$ touch 'a1\' a2 ' spaces '
$ # CORRECT RESULT
$ for f in *; do printf ':%s:\n' "$f"; done
:a1\:
:a2:
: spaces :
$ # ERRONEOUS HANDLING OF LEADING/TRAILING WHITESPACE AND TRAILING BACKSLASH
$ ls | while read f; do printf ':%s:\n' "$f"; done
:a1a2:
:spaces:
$ # FIX ONLY THE BACKSLASH
$ ls | while read -r f; do printf ':%s:\n' "$f"; done
:a1\:
:a2:
:spaces:
$ # FIX ONLY THE SPACES
$ ls | while IFS= read f; do printf ':%s:\n' "$f"; done
:a1a2:
: spaces :
$ # FIX BOTH
$ ls | while IFS= read -r f; do printf ':%s:\n' "$f"; done
:a1\:
:a2:
: spaces :
You are correct in that there may be a limit to how many files the pathname expansion in the for-loop list can handle, but if it's sufficient (usually is) for the task at hand, it's the simplest and safest method.
You are mistaken about the for f in * ... construct. Since pathname expansion occurs after field splitting, the expansion of * is absolutely safe with regard to IFS characters (by default, space, tab, and newline).
I've always thought it was the other way round -- my twisted reasoning was that the shell had to expand the glob before it could split fields otherwise all files resulting from * would be treated as a single token.
Quote:
Originally Posted by alister
Ironically, the statement you replaced it with does not handle spaces correctly in all cases. If ls prints a filename with leading or trailing spaces, read will discard those, yielding either a non-existent file or a different file. Further, if the filename ended with a backslash, that backslash would be stripped and the next filename in the list, if any, would be appended. while IFS= read -r f fixes both issues.
Very embarrassing -- I wasn't even thinking along the lines of lead/trailing spaces.
Appreciate your pointing these out, and the samples. Fortunately, I'm always in learning mode
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