Files in the directory look like that:
A_1_email.txt
A_1_phone.txt
A_2_email.txt
A_2_phone.txt
B_1_email.txt
B_1_phone.txt
B_2_email.txt
B_2_phone.txt
What I want:
To merge files A_1_email.txt and A_1_phone.txt; to merge files B_1_email.txt and B_1_phone.txt and so on.
What I mean by that: if first to flags of files names matches (for example A to A; 1 to 1) than merge files.
How I tried to do this:
ls * | cut -d "_" -f 1-2 | sort | uniq -c | awk '{print $2}' > names && for name in
$(cat names); do
And I am lost here, really don't know how should I go on further.
The following are based on #MichaelJ.Barber's answer (which had the excellent idea of using join), but with the specific intention to avoid the dangerous practice of parsing the output of ls:
# Simple loop: avoids subshells, pipelines
for file in *_email.txt; do
if [[ -r "$file" && -r "${file%_*}_phone.txt" ]]; then
join "$file" "${file%_*}_phone.txt"
fi
done
or
##
# Use IFS and a function to avoid contaminating the global environment.
joinEmailPhone() {
local IFS=$'\n'
local -x LC_COLLATE=C # Ensure glob expansion sorting makes sense.
# According to `man (1) bash`, globs expand sorted "alphabetically".
# If we use LC_COLLATE=C, we don't need to sort again.
# Use an awk test (!seen[$0]++) to ensure uniqueness and a parameter expansion instead of cut
awk '!seen[$0]++{ printf("join %s_email.txt %s_phone.txt\n", $1, $1) }' <<< "${*%_*}" | sh
}
joinEmailPhone *
But in all probability (again assuming LC_COLLATE=C) you can get away with:
printf 'join %s %s\n' * | sh
I'll assume that the files all have tab-separated name-value pairs, where the value is email or phone as appropriate. If that's not the case, do some pre-sorting or otherwise modify as appropriate.
ls *_{email,phone}.txt |
cut -d "_" -f1-2 | # could also do this with variable expansion
sort -u |
awk '{ printf("join %s_email.txt %s_phone.txt\n", $1, $1) }' |
sh
What this does is to identify the unique prefixes for the files and use 'awk' to generate shell commands for joining the pairs, which are then piped into sh to actually run the commands.
You may use printf '%s\n' *_{email,phone}.txt | ... instead of ls *-... in the given scenario, i. e. no newline chars in file path names are to be expected. At least one external command less!
Use a for loop to iterate over the email files, using the read command
with the proper value of IFS to split the file name into the necessary parts.
Note that this does use one non-POSIX feature that bash provides, namely
using a here-string (<<<) to pass the value of $email to the read command.
for email in *_email.txt; do
IFS=_ read fst snd <<< $email
phone=${fst}_${snd}_phone.txt
# merge $email and $phone
done
Related
I'm trying to do a simple bash Script to check if there is a not unique UID in /etc/passwd.
I did a script already to display all the UID but I can't figure out how to compare them and return the not unique one if it exists.
Here is the script I wrote:
#!/bin/bash
passwd="$(cat /etc/passwd)"
while read -r line; do
IFS=':' read -ra arrayPasswd <<< "$line"
echo ${arrayPasswd[2]}
done <<< "$passwd"
How could I compare them and return the not unique one in case there is one ?
If you have a script that outputs all of your UIDs, you can use sort and uniq programs to get the desired result:
$ your-script | sort | uniq -d
uniq program takes some lines and deletes consecutive repeats. Flag -d makes it output only duplicates and delete unique ones. You need to use sort first to make any repetitions consecutive.
With awk:
$ awk -F: 'a[$3]++==1 { print $3 }' /etc/passwd
Explanation:
In an associative array (a.k.a. dictionary), keep a count of occurrences of UIDs.
If any UID is repeated, print it.
I am interested in concatenate many files together based on the numeric number and also remove the first line.
e.g. chr1_smallfiles then chr2_smallfiles then chr3_smallfiles.... etc (each without the header)
Note that chr10_smallfiles needs to come after chr9_smallfiles -- that is, this needs to be numeric sort order.
When separate the two command awk and ls -v1, each does the job properly, but when put them together, it doesn't work. Please help thanks!
awk 'FNR>1' | ls -v1 chr*_smallfiles > bigfile
The issue is with the way that you're trying to pass the list of files to awk. At the moment, you're piping the output of awk to ls, which makes no sense.
Bear in mind that, as mentioned in the comments, ls is a tool for interactive use, and in general its output shouldn't be parsed.
If sorting weren't an issue, you could just use:
awk 'FNR > 1' chr*_smallfiles > bigfile
The shell will expand the glob chr*_smallfiles into a list of files, which are passed as arguments to awk. For each filename argument, all but the first line will be printed.
Since you want to sort the files, things aren't quite so simple. If you're sure the full range of files exist, just replace chr*_smallfiles with chr{1..99}_smallfiles in the original command.
Using some Bash-specific and GNU sort features, you can also achieve the sorting like this:
printf '%s\0' chr*_smallfiles | sort -z -n -k1.4 | xargs -0 awk 'FNR > 1' > bigfile
printf '%s\0' prints each filename followed by a null-byte
sort -z sorts records separated by null-bytes
-n -k1.4 does a numeric sort, starting from the 4th character (the numeric part of the filename)
xargs -0 passes the sorted, null-separated output as arguments to awk
Otherwise, if you want to go through the files in numerical order, and you're not sure whether all the files exist, then you can use a shell loop (although it'll be significantly slower than a single awk invocation):
for file in chr{1..99}_smallfiles; do # 99 is the maximum file number
[ -f "$file" ] || continue # skip missing files
awk 'FNR > 1' "$file"
done > bigfile
You can also use tail to concatenate all the files without header
tail -q -n+2 chr*_smallfiles > bigfile
In case you want to concatenate the files in a natural sort order as described in your quesition, you can pipe the result of ls -v1 to xargs using
ls -v1 chr*_smallfiles | xargs -d $'\n' tail -q -n+2 > bigfile
(Thanks to Charles Duffy) xargs -d $'\n' sets the delimiter to a newline \n in case the filename contains white spaces or quote characters
Using a bash 4 associative array to extract only the numeric substring of each filename; sort those individually; and then retrieve and concatenate the full names in the resulting order:
#!/usr/bin/env bash
case $BASH_VERSION in ''|[123].*) echo "Requires bash 4.0 or newer" >&2; exit 1;; esac
# when this is done, you'll have something like:
# files=( [1]=chr_smallfiles1.txt
# [10]=chr_smallfiles10.txt
# [9]=chr_smallfiles9.txt )
declare -A files=( )
for f in chr*_smallfiles.txt; do
files[${f//[![:digit:]]/}]=$f
done
# now, emit those indexes (1, 10, 9) to "sort -n -z" to sort them as numbers
# then read those numbers, look up the filenames associated, and pass to awk.
while read -r -d '' key; do
awk 'FNR > 1' <"${files[$key]}"
done < <(printf '%s\0' "${!files[#]}" | sort -n -z) >bigfile
You can do with a for loop like below, which is working for me:-
for file in chr*_smallfiles
do
tail +2 "$file" >> bigfile
done
How will it work? For loop read all the files from current directory with wild chard character * chr*_smallfiles and assign the file name to variable file and tail +2 $file will output all the lines of that file except the first line and append in file bigfile. So finally all files will be merged (accept the first line of each file) into one i.e. file bigfile.
Just for completeness, how about a sed solution?
for file in chr*_smallfiles
do
sed -n '2,$p' $file >> bigfile
done
Hope it helps!
Suppose echo $PATH yields /first/dir:/second/dir:/third/dir.
Question: How does one echo the contents of $PATH one directory at a time as in:
$ newcommand $PATH
/first/dir
/second/dir
/third/dir
Preferably, I'm trying to figure out how to do this with a for loop that issues one instance of echo per instance of a directory in $PATH.
echo "$PATH" | tr ':' '\n'
Should do the trick. This will simply take the output of echo "$PATH" and replaces any colon with a newline delimiter.
Note that the quotation marks around $PATH prevents the collapsing of multiple successive spaces in the output of $PATH while still outputting the content of the variable.
As an additional option (and in case you need the entries in an array for some other purpose) you can do this with a custom IFS and read -a:
IFS=: read -r -a patharr <<<"$PATH"
printf %s\\n "${patharr[#]}"
Or since the question asks for a version with a for loop:
for dir in "${patharr[#]}"; do
echo "$dir"
done
How about this:
echo "$PATH" | sed -e 's/:/\n/g'
(See sed's s command; sed -e 'y/:/\n/' will also work, and is equivalent to the tr ":" "\n" from some other answers.)
It's preferable not to complicate things unless absolutely necessary: a for loop is not needed here. There are other ways to execute a command for each entry in the list, more in line with the Unix Philosophy:
This is the Unix philosophy: Write programs that do one thing and do it well. Write programs to work together. Write programs to handle text streams, because that is a universal interface.
such as:
echo "$PATH" | sed -e 's/:/\n/g' | xargs -n 1 echo
This is functionally equivalent to a for-loop iterating over the PATH elements, executing that last echo command for each element. The -n 1 tells xargs to supply only 1 argument to it's command; without it we would get the same output as echo "$PATH" | sed -e 'y/:/ /'.
Since this uses xargs, which has built-in support to split the input, and echoes the input if no command is given, we can write that as:
echo -n "$PATH" | xargs -d ':' -n 1
The -d ':' tells xargs to use : to separate it's input rather than a newline, and the -n tells /bin/echo to not write a newline, otherwise we end up with a blank trailing line.
here is another shorter one:
echo -e ${PATH//:/\\n}
You can use tr (translate) to replace the colons (:) with newlines (\n), and then iterate over that in a for loop.
directories=$(echo $PATH | tr ":" "\n")
for directory in $directories
do
echo $directory
done
My idea is to use echo and awk.
echo $PATH | awk 'BEGIN {FS=":"} {for (i=0; i<=NF; i++) print $i}'
EDIT
This command is better than my former idea.
echo "$PATH" | awk 'BEGIN {FS=":"; OFS="\n"} {$1=$1; print $0}'
If you can guarantee that PATH does not contain embedded spaces, you can:
for dir in ${PATH//:/ }; do
echo $dir
done
If there are embedded spaces, this will fail badly.
# preserve the existing internal field separator
OLD_IFS=${IFS}
# define the internal field separator to be a colon
IFS=":"
# do what you need to do with $PATH
for DIRECTORY in ${PATH}
do
echo ${DIRECTORY}
done
# restore the original internal field separator
IFS=${OLD_IFS}
I have a file containing a list of replacement pairs (about 100 of them) which are used by sed to replace strings in files.
The pairs go like:
old|new
tobereplaced|replacement
(stuffiwant).*(too)|\1\2
and my current code is:
cat replacement_list | while read i
do
old=$(echo "$i" | awk -F'|' '{print $1}') #due to the need for extended regex
new=$(echo "$i" | awk -F'|' '{print $2}')
sed -r "s/`echo "$old"`/`echo "$new"`/g" -i file
done
I cannot help but think that there is a more optimal way of performing the replacements. I tried turning the loop around to run through lines of the file first but that turned out to be much more expensive.
Are there any other ways of speeding up this script?
EDIT
Thanks for all the quick responses. Let me try out the various suggestions before choosing an answer.
One thing to clear up: I also need subexpressions/groups functionality. For example, one replacement I might need is:
([0-9])U|\10 #the extra brackets and escapes were required for my original code
Some details on the improvements (to be updated):
Method: processing time
Original script: 0.85s
cut instead of awk: 0.71s
anubhava's method: 0.18s
chthonicdaemon's method: 0.01s
You can use sed to produce correctly -formatted sed input:
sed -e 's/^/s|/; s/$/|g/' replacement_list | sed -r -f - file
I recently benchmarked various string replacement methods, among them a custom program, sed -e, perl -lnpe and an probably not that widely known MySQL command line utility, replace. replace being optimized for string replacements was almost an order of magnitude faster than sed. The results looked something like this (slowest first):
custom program > sed > LANG=C sed > perl > LANG=C perl > replace
If you want performance, use replace. To have it available on your system, you'll need to install some MySQL distribution, though.
From replace.c:
Replace strings in textfile
This program replaces strings in files or from stdin to stdout. It accepts a list of from-string/to-string pairs and replaces each occurrence of a from-string with the corresponding to-string. The first occurrence of a found string is matched. If there is more than one possibility for the string to replace, longer matches are preferred before shorter matches.
...
The programs make a DFA-state-machine of the strings and the speed isn't dependent on the count of replace-strings (only of the number of replaces). A line is assumed ending with \n or \0. There are no limit exept memory on length of strings.
More on sed. You can utilize multiple cores with sed, by splitting your replacements into #cpus groups and then pipe them through sed commands, something like this:
$ sed -e 's/A/B/g; ...' file.txt | \
sed -e 's/B/C/g; ...' | \
sed -e 's/C/D/g; ...' | \
sed -e 's/D/E/g; ...' > out
Also, if you use sed or perl and your system has an UTF-8 setup, then it also boosts performance to place a LANG=C in front of the commands:
$ LANG=C sed ...
You can cut down unnecessary awk invocations and use BASH to break name-value pairs:
while IFS='|' read -r old new; do
# echo "$old :: $new"
sed -i "s~$old~$new~g" file
done < replacement_list
IFS='|' will give enable read to populate name-value in 2 different shell variables old and new.
This is assuming ~ is not present in your name-value pairs. If that is not the case then feel free to use an alternate sed delimiter.
Here is what I would try:
store your sed search-replace pair in a Bash array like ;
build your sed command based on this array using parameter expansion
run command.
patterns=(
old new
tobereplaced replacement
)
pattern_count=${#patterns[*]} # number of pattern
sedArgs=() # will hold the list of sed arguments
for (( i=0 ; i<$pattern_count ; i=i+2 )); do # don't need to loop on the replacement…
search=${patterns[i]};
replace=${patterns[i+1]}; # … here we got the replacement part
sedArgs+=" -e s/$search/$replace/g"
done
sed ${sedArgs[#]} file
This result in this command:
sed -e s/old/new/g -e s/tobereplaced/replacement/g file
You can try this.
pattern=''
cat replacement_list | while read i
do
old=$(echo "$i" | awk -F'|' '{print $1}') #due to the need for extended regex
new=$(echo "$i" | awk -F'|' '{print $2}')
pattern=${pattern}"s/${old}/${new}/g;"
done
sed -r ${pattern} -i file
This will run the sed command only once on the file with all the replacements. You may also want to replace awk with cut. cut may be more optimized then awk, though I am not sure about that.
old=`echo $i | cut -d"|" -f1`
new=`echo $i | cut -d"|" -f2`
You might want to do the whole thing in awk:
awk -F\| 'NR==FNR{old[++n]=$1;new[n]=$2;next}{for(i=1;i<=n;++i)gsub(old[i],new[i])}1' replacement_list file
Build up a list of old and new words from the first file. The next ensures that the rest of the script isn't run on the first file. For the second file, loop through the list of replacements and perform them each one by one. The 1 at the end means that the line is printed.
{ cat replacement_list;echo "-End-"; cat YourFile; } | sed -n '1,/-End-/ s/$/³/;1h;1!H;$ {g
t again
:again
/^-End-³\n/ {s///;b done
}
s/^\([^|]*\)|\([^³]*\)³\(\n\)\(.*\)\1/\1|\2³\3\4\2/
t again
s/^[^³]*³\n//
t again
:done
p
}'
More for fun to code via sed. Try maybe for a time perfomance because this start only 1 sed that is recursif.
for posix sed (so --posix with GNU sed)
explaination
copy replacement list in front of file content with a delimiter (for line with ³ and for list with -End-) for an easier sed handling (hard to use \n in class character in posix sed.
place all line in buffer (add the delimiter of line for replacement list and -End- before)
if this is -End-³, remove the line and go to final print
replace each first pattern (group 1) found in text by second patttern (group 2)
if found, restart (t again)
remove first line
restart process (t again). T is needed because b does not reset the test and next t is always true.
Thanks to #miku above;
I have a 100MB file with a list of 80k replacement-strings.
I tried various combinations of sed's sequentially or parallel, but didn't see throughputs getting shorter than about a 20-hour runtime.
Instead I put my list into a sequence of scripts like "cat in | replace aold anew bold bnew cold cnew ... > out ; rm in ; mv out in".
I randomly picked 1000 replacements per file, so it all went like this:
# first, split my replace-list into manageable chunks (89 files in this case)
split -a 4 -l 1000 80kReplacePairs rep_
# next, make a 'replace' script out of each chunk
for F in rep_* ; do \
echo "create and make executable a scriptfile" ; \
echo '#!/bin/sh' > run_$F.sh ; chmod +x run_$F.sh ; \
echo "for each chunk-file line, strip line-ends," ; \
echo "then with sed, turn '{long list}' into 'cat in | {long list}' > out" ; \
cat $F | tr '\n' ' ' | sed 's/^/cat in | replace /;s/$/ > out/' >> run_$F.sh ;
echo "and append commands to switch in and out files, for next script" ; \
echo -e " && \\\\ \nrm in && mv out in\n" >> run_$F.sh ; \
done
# put all the replace-scripts in sequence into a main script
ls ./run_rep_aa* > allrun.sh
# make it executable
chmod +x allrun.sh
# run it
nohup ./allrun.sh &
.. which ran in under 5 mins, a lot less than 20 hours !
Looking back, I could have used more pairs per script, by finding how many lines would make up the limit.
xargs --show-limits </dev/null 2>&1 | grep --color=always "actually use:"
Maximum length of command we could actually use: 2090490
So just under 2MB; how many pairs would that be for my script ?
head -c 2090490 80kReplacePairs | wc -l
76923
So it seems I could have used 2 * 40000-line chunks
to expand on chthonicdaemon's solution
live demo
#! /bin/sh
# build regex from text file
REGEX_FILE=some-patch.regex.diff
# test
# set these with "export key=val"
SOME_VAR_NAME=hello
ANOTHER_VAR_NAME=world
escape_b() {
echo "$1" | sed 's,/,\\/,g'
}
regex="$(
(echo; cat "$REGEX_FILE"; echo) \
| perl -p -0 -e '
s/\n#[^\n]*/\n/g;
s/\(\(SOME_VAR_NAME\)\)/'"$(escape_b "$SOME_VAR_NAME")"'/g;
s/\(\(ANOTHER_VAR_NAME\)\)/'"$(escape_b "$ANOTHER_VAR_NAME")"'/g;
s/([^\n])\//\1\\\//g;
s/\n-([^\n]+)\n\+([^\n]*)(?:\n\/([^\n]+))?\n/s\/\1\/\2\/\3;\n/g;
'
)"
echo "regex:"; echo "$regex" # debug
exec perl -00 -p -i -e "$regex" "$#"
prefixing lines with -+/ allows empty "plus" values, and protects leading whitespace from buggy text editors
sample input: some-patch.regex.diff
# file format is similar to diff/patch
# this is a comment
# replace all "a/a" with "b/b"
-a/a
+b/b
/g
-a1|a2
+b1|b2
/sg
# this is another comment
-(a1).*(a2)
+b\1b\2b
-a\na\na
+b
-a1-((SOME_VAR_NAME))-a2
+b1-((ANOTHER_VAR_NAME))-b2
sample output
s/a\/a/b\/b/g;
s/a1|a2/b1|b2/;;
s/(a1).*(a2)/b\1b\2b/;
s/a\na\na/b/;
s/a1-hello-a2/b1-world-b2/;
this regex format is compatible with sed and perl
since miku mentioned mysql replace:
replacing fixed strings with regex is non-trivial,
since you must escape all regex chars,
but you also must handle backslash escapes ...
naive escaper:
echo '\(\n' | perl -p -e 's/([.+*?()\[\]])/\\\1/g'
\\(\n
I have two strings and I want to split with space and use them two by two:
namespaces="Calc Fs"
files="calc.hpp fs.hpp"
for example, I want to use like this: command -q namespace[i] -l files[j]
I'm a noob in Bourne Shell.
Put them into an array like so:
#!/bin/bash
namespaces="Calc Fs"
files="calc.hpp fs.hpp"
i=1
j=0
name_arr=( $namespaces )
file_arr=( $files )
command -q "${name_arr[i]}" -l "${file_arr[j]}"
echo "hello world" | awk '{split($0, array, " ")} END{print array[2]}'
is how you would split a simple string.
if what you want to do is loop through combinations of the two split strings, then you want something like this:
for namespace in $namespaces
do
for file in $files
do
command -q $namespace -l $file
done
done
EDIT:
or to expand on the awk solution that was posted, you could also just do:
echo $foo | awk '{print $'$i'}'
EDIT 2:
Disclaimer: I don not profess to be any kind of expert in awk at all, so there may be small errors in this explanation.
Basically what the snippet above does is pipe the contents of $foo into the standard input of awk. Awk reads from it's standard in line by line, separating each line into fields based on a field separator, which is any number of spaces by default. Awk executes the program that it is given as an argument. In this case, the shell expands '{ print $'$1' }' into { print $1 } which simply tells awk to print field number 1 of each line of its input.
If you want to learn more I think that this blog post does a pretty good job of describing the basics (as well as the basics of sed and grep) if you skip past the more theoretical stuff at the start (unless you're into that kind of thing).
I wanted to find a way to do it without arrays, here it is:
paste -d " " <(tr " " "\n" <<< $namespaces) <(tr " " "\n" <<< $files) |
while read namespace file; do
command -q $namespace -l $file
done
Two special usage here: process substitution (<(...)) and here strings (<<<). Here strings are a shortcut for echo $namespaces | tr " " "\n". Process substitution is a shortcut for fifo creation, it allows paste to be run using the output of commands instead of files.
If you are using zsh this could be very easy:
files="calc.hpp fs.hpp"
# all elements
print -l ${(s/ /)files}
# just the first one
echo ${${(s/ /)files}[1]} # just the first one