Grep (Bash) error - bash

I have a file like this called new.samples.dat
-4.5000000000E-01 8.0000000000E+00 -1.3000000000E-01
5.0000000000E-02 8.0000000000E+00 3.4000000000E-01
...
I have to search all this numbers of this file in another file called Remaining.Simulations.dat and copy them in another file. I did like this
for sample_index in $(seq 1 100)
do
sample=$(awk 'NR=='$sample_index'' new.samples.dat)
grep "$sample" Remaining.Simulations.dat >> Previous.Training.dat
done
It works almost fine but it does not copy all the $sample into Previous.Training.dat even if I am sure that these are in Remaining.Simulations.dat
This errors appear
grep: invalid option -- '.'
Usage: grep [OPTION]... PATTERN [FILE]...
Try `grep --help' for more information.
Do you have any idea how to solve it?Thank you

It's because you're trying to grep for something like -4.5 and grep is treating that as an option rather than a search string. If you use -- to indicate there are no more options, this should work okay:
pax> echo -4.5000000000E-01 | grep -4.5000000000E-01
grep: invalid option -- '.'
Usage: grep [OPTION]... PATTERN [FILE]...
Try 'grep --help' for more information.
pax> echo -4.5000000000E-01 | grep -- -4.5000000000E-01
-4.5000000000E-01
In addition, if you pass the string 7.2 to grep, it will match any line containing 7 followed by any character followed by 2 since:
Regular expressions treat . as a special character; and
Without start and end markers, 7.2 will also match 47.2, 7.25 and so on.

With awk you can try something like:
awk '
NR==FNR {
for (i=1;i<=NF;i++) {
numbers[$i]++
}
next
}
{
for (number in numbers)
if (index ($0,number) > 0) {
print $0
}
}' new.samples.dat Remaining.Simulations.dat > anotherfile

Related

grep of string that includes a tilde returns non-matching lines

I'm trying to search for a specific string in a file. The string includes a tilde- I am trying to isolate the line that contains the string "~ ca_cert".
This is my script:
#!/bin/bash
LIST=("~ ca_cert" "backup_window")
FILE=./test
for x in "${LIST[#]}"; do
grep $x $FILE
done
When I run it, it returns other lines that contain tildes. For example, in a file that contains the following, it return all of the lines, when my intention is for it to only return the bottom line that contains ~ ca_cert:
./test:./terraform.tfplan: ~ update in-place
./test:./terraform.tfplan: ~ resource "aws_db_instance" "rds_instance" {
./test:./terraform.tfplan: ~ ca_cert_identifier = "rds-ca-2019" -> "rds-ca-2015"
Problem is not quoting pattern i.e. $x in your grep command. That basically runs your command as grep '~' ca_cert ./test and finds all the lines matching ~ with an error.
However you don't really need to run a loop here. Just use grep -f with process substitution:
grep -Ff <(printf '%s\n' "${LIST[#]}") ./test
./terraform.tfplan: ~ ca_cert_identifier = "rds-ca-2019" -> "rds-ca-2015"

Multiline CSV: output on a single line, with double-quoted input lines, using a different separator

I'm trying to get a multiline output from a CSV into one line in Bash.
My CSV file looks like this:
hi,bye
hello,goodbye
The end goal is for it to look like this:
"hi/bye", "hello/goodbye"
This is currently where I'm at:
INPUT=mycsvfile.csv
while IFS=, read col1 col2 || [ -n "$col1" ]
do
source=$(awk '{print;}' | sed -e 's/,/\//g' )
echo "$source";
done < $INPUT
The output is on every line and I'm able to change the , to a / but I'm not sure how to put the output on one line with quotes around it.
I've tried BEGIN:
source=$(awk 'BEGIN { ORS=", " }; {print;}'| sed -e 's/,/\//g' )
But this only outputs the last line, and omits the first hi/bye:
hello/goodbye
Would anyone be able to help me?
Just do the whole thing (mostly) in awk. The final sed is just here to trim some trailing cruft and inject a newline at the end:
< mycsvfile.csv awk '{print "\""$1, $2"\""}' FS=, OFS=/ ORS=", " | sed 's/, $//'
If you're willing to install trl, a utility of mine, the command can be simplified as follows:
input=mycsvfile.csv
trl -R '| ' < "$input" | tr ',|' '/,'
trl transforms multiline input into double-quoted single-line output separated by ,<space> by default.
-R '| ' (temporarily) uses |<space> as the separator instead; this assumes that your data doesn't contain | instances, but you can choose any char. that you know not be part of your data.
tr ',|' '/,' then translates all , instances (field-internal to the input lines) into / instances, and all | instances (the temporary separator) into , instances, yielding the overall result as desired.
Installation of trl from the npm registry (Linux and macOS)
Note: Even if you don't use Node.js, npm, its package manager, works across platforms and is easy to install; try
curl -L https://git.io/n-install | bash
With Node.js installed, install as follows:
[sudo] npm install trl -g
Note:
Whether you need sudo depends on how you installed Node.js and whether you've changed permissions later; if you get an EACCES error, try again with sudo.
The -g ensures global installation and is needed to put trl in your system's $PATH.
Manual installation (any Unix platform with bash)
Download this bash script as trl.
Make it executable with chmod +x trl.
Move it or symlink it to a folder in your $PATH, such as /usr/local/bin (macOS) or /usr/bin (Linux).
$ awk -F, -v OFS='/' -v ORS='"' '{$1=s ORS $1; s=", "; print} END{printf RS}' file
"hi/bye", "hello/goodbye"
There is no need for a bash loop, which is invariably slow.
sed and tr can do this more efficiently:
input=mycsvfile.csv
sed 's/,/\//g; s/.*/"&", /; $s/, $//' "$input" | tr -d '\n'
s/,/\//g uses replaces all (g) , instances with / instances (escaped as \/ here).
s/.*/"&", / encloses the resulting line in "...", followed by ,<space>:
regex .* matches the entire pattern space (the potentially modified input line)
& in the replacement string represent that match.
$s/, $// removes the undesired trailing ,<space> from the final line ($)
tr -d '\n' then simply removes the newlines (\n) from the result, because sed invariably outputs each line with a trailing newline.
Note that the above command's single-line output will not have a trailing newline; simply append ; printf '\n' if it is needed.
In awk:
$ awk '{sub(/,/,"/");gsub(/^|$/,"\"");b=b (NR==1?"":", ")$0}END{print b}' file
"hi/bye", "hello/goodbye"
Explained:
$ awk '
{
sub(/,/,"/") # replace comma
gsub(/^|$/,"\"") # add quotes
b=b (NR==1?"":", ") $0 # buffer to add delimiters
}
END { print b } # output
' file
I'm assuming you just have 2 lines in your file? If you have alternating 2 line pairs, let me know in comments and I will expand for that general case. Here is a one-line awk conversion for you:
# NOTE: I am using the octal ascii code for the
# double quote char (\42=") in my printf statement
$ awk '{gsub(/,/,"/")}NR==1{printf("\42%s\42, ",$0)}NR==2{printf("\42%s\42\n",$0)}' file
output:
"hi/bye", "hello/goodbye"
Here is my attempt in awk:
awk 'BEGIN{ ORS = " " }{ a++; gsub(/,/, "/"); gsub(/[a-z]+\/[a-z]+/, "\"&\""); print $0; if (a == 1){ print "," }}{ if (a==2){ printf "\n"; a = 0 } }'
Works also if your Input has more than two lines.If you need some explanation feel free to ask :)

Grep for Keyword1Keyword2 but not Keyword1TEXTKeyword2 - Very large grep

I want to be able to grep for exact match results without outputting those with text in between my searched words. the middle being part of the output. For example:
egrep -i "^cat|^dog" list.txt >> startswith.txt
egrep -i "home$|house$" startswith.txt >> final.txt
I want this to return any matches for cathome, cathouse, doghome, doghouse; but not return cathasahome, catneedsahouse, etc. Take note that the files would be wayyy to big for me to go through and say ^word1word2$ in every combination.
Is there a way to do this within grep or egrep.
Use some grouping to specify both parts of your pattern, The anchors (^ and $) will apply to the groups.
$ cat list.txt
cathome
cathouse
catindahouse
dogindahome
doghouse
doghome
$ egrep -i "^(dog|cat)(home|house)$" list.txt
cathome
cathouse
doghouse
doghome
You could try the same thing in Perl regex mode, with non-capturing groups (since you don't care about capturing them):
$ grep -Pi "^(?:dog|cat)(?:home|house)$" list.txt
No idea if that'll make a difference either way, but doesn't hurt to try.
You didn't provide any sample input or expected output so this is an untested guess but this is probably what you're looking for:
awk '
BEGIN {
split("cat dog",beg)
split("home house",end)
for (i in beg)
for (j in end)
matches[beg[i] end[j]]
}
tolower($0) in matches
' file
e.g.:
$ cat file
acathome
CatHome
catinhouse
CATHOUSE
doghomes
dogHOME
dogathouse
DOGhouse
$ awk '
BEGIN {
split("cat dog",beg)
split("home house",end)
for (i in beg)
for (j in end)
matches[beg[i] end[j]]
}
tolower($0) in matches
' file
CatHome
CATHOUSE
dogHOME
DOGhouse

Multi-line grep with positive and negative filtering

I need to grep for a multi-line string that doesn't include one string, but does include others. This is what I'm searching for in some HTML files:
<not-this>
<this> . . . </this>
</not-this>
In other words, I want to find files that contain <this> and </this> on the same line, but should not be surrounded by html tags <not-this> on the lines before and/or after. Here is some shorthand logic for what I want to do:
grep 'this' && '/this' && !('not-this')
I've seen answers with the following...
grep -Er -C 2 '.*this.*this.*' . | grep -Ev 'not-this'
...but this just erases the line(s) containing the "not" portion, and displays the other lines. What I'd like is for it to not pull those results at all if "not-this" is found within a line or two of "this".
Is there a way to accomplish this?
P.S. I'm using Ubuntu and gnome-terminal.
It sounds like an awk script might work better here:
$ cat input.txt
<not-this>
<this>BAD! DO NOT PRINT!</this>
</not-this>
<yes-this>
<this>YES! PRINT ME!</this>
</yes-this>
$ cat not-this.awk
BEGIN {
notThis=0
}
/<not-this>/ {notThis=1}
/<\/not-this>/ {notThis=0}
/<this>.*<\/this>/ {if (notThis==0) print}
$ awk -f not-this.awk input.txt
<this>YES! PRINT ME!</this>
Or, if you'd prefer, you can squeeze this awk script onto one long line:
$ awk 'BEGIN {notThis=0} /<not-this>/ {notThis=1} /<\/not-this>/ {notThis=0} /<this>.*<\/this>/ {if (notThis==0) print}' input.txt

Bash command to extract characters in a string

I want to write a small script to generate the location of a file in an NGINX cache directory.
The format of the path is:
/path/to/nginx/cache/d8/40/32/13febd65d65112badd0aa90a15d84032
Note the last 6 characters: d8 40 32, are represented in the path.
As an input I give the md5 hash (13febd65d65112badd0aa90a15d84032) and I want to generate the output: d8/40/32/13febd65d65112badd0aa90a15d84032
I'm sure sed or awk will be handy, but I don't know yet how...
This awk can make it:
awk 'BEGIN{FS=""; OFS="/"}{print $(NF-5)$(NF-4), $(NF-3)$(NF-2), $(NF-1)$NF, $0}'
Explanation
BEGIN{FS=""; OFS="/"}. FS="" sets the input field separator to be "", so that every char will be a different field. OFS="/" sets the output field separator as /, for print matters.
print ... $(NF-1)$NF, $0 prints the penultimate field and the last one all together; then, the whole string. The comma is "filled" with the OFS, which is /.
Test
$ awk 'BEGIN{FS=""; OFS="/"}{print $(NF-5)$(NF-4), $(NF-3)$(NF-2), $(NF-1)$NF, $0}' <<< "13febd65d65112badd0aa90a15d84032"
d8/40/32/13febd65d65112badd0aa90a15d84032
Or with a file:
$ cat a
13febd65d65112badd0aa90a15d84032
13febd65d65112badd0aa90a15f1f2f3
$ awk 'BEGIN{FS=""; OFS="/"}{print $(NF-5)$(NF-4), $(NF-3)$(NF-2), $(NF-1)$NF, $0}' a
d8/40/32/13febd65d65112badd0aa90a15d84032
f1/f2/f3/13febd65d65112badd0aa90a15f1f2f3
With sed:
echo '13febd65d65112badd0aa90a15d84032' | \
sed -n 's/\(.*\([0-9a-f]\{2\}\)\([0-9a-f]\{2\}\)\([0-9a-f]\{2\}\)\)$/\2\/\3\/\4\/\1/p;'
Having GNU sed you can even simplify the pattern using the -r option. Now you won't need to escape {} and () any more. Using ~ as the regex delimiter allows to use the path separator / without need to escape it:
sed -nr 's~(.*([0-9a-f]{2})([0-9a-f]{2})([0-9a-f]{2}))$~\2/\3/\4/\1~p;'
Output:
d8/40/32/13febd65d65112badd0aa90a15d84032
Explained simple the pattern does the following: It matches:
(all (n-5 - n-4) (n-3 - n-2) (n-1 - n-0))
and replaces it by
/$1/$2/$3/$0
You can use a regular expression to separate each of the last 3 bytes from the rest of the hash.
hash=13febd65d65112badd0aa90a15d84032
[[ $hash =~ (..)(..)(..)$ ]]
new_path="/path/to/nginx/cache/${BASH_REMATCH[1]}/${BASH_REMATCH[2]}/${BASH_REMATCH[3]}/$hash"
Base="/path/to/nginx/cache/"
echo '13febd65d65112badd0aa90a15d84032' | \
sed "s|\(.*\(..\)\(..\)\(..\)\)|${Base}\2/\3/\4/\1|"
# or
# sed sed 's|.*\(..\)\(..\)\(..\)$|${Base}\1/\2/\3/&|'
Assuming info is a correct MD5 (and only) string
First of all - thanks to all of the responders - this was extremely quick!
I also did my own scripting meantime, and came up with this solution:
Run this script with a parameter of the URL you're looking for (www.example.com/article/76232?q=hello for example)
#!/bin/bash
path=$1
md5=$(echo -n "$path" | md5sum | cut -f1 -d' ')
p3=$(echo "${md5:0-2:2}")
p2=$(echo "${md5:0-4:2}")
p1=$(echo "${md5:0-6:2}")
echo "/path/to/nginx/cache/$p1/$p2/$p3/$md5"
This assumes the NGINX cache has a key structure of 2:2:2.

Resources