I need to modify the 5 to 9 column directly in each line from a file.
Currently i'm doing this in a while loop, getting each column by line.
For example a line looks like:
echo "m.mustermann#muster.com;surnanme;givenname;displayname;1111;2222;3333;44(#44;(5555"
line_9=$(echo $line | awk -F "[;]" '{print $9}' | sed 's/[^0-9+*,]*//g')
Is there a possibility to do that with "sed -i" instead of awk
Thanks for any help
I'm not sure it can be done generally in sed, but you could definitely do it in awk:
… | awk -F";" '{ gsub("[^0-9]*","",$9); print $9 }'
If you really want to do it with sed, the expression will look something like:
… | sed -e 's,\(^[^;]*;[^;]*;[^;]*;[^;]*;[^;]*;[^;]*;[^;]*;[^;]*;[0-9]*\)[^0-9]*\([0-9]*\)[^0-9]*\([0-9]*\)[^0-9]*\([0-9]*\)[^0-9]*\([0-9]*\)[^0-9]*\([0-9]*\)[^0-9]*\([0-9]*\)[^0-9]*\([0-9]*\)[^0-9]*\([0-9]*\)\(.*\),\1\2\3\4\5\6\7\8\9,'
For a version with sed (posix) only
line_9="$(echo $line | sed 'H;x;s/^\(.\)\(\([^;]*;\)\{8\}\)\([^;]*\)/\2\1\4\1/;h;s/\(\n\).*\1/\1/;x;s/.*\(\n\)\(.*\)\1.*/\2/;s/[^0-9+*,]*//g;G;s/\(.*\)\(\n\)\(.*\)\2/\3\1/;h;s/.*//;x' )"
Related
I have a simple .csv file with lines that holds 't' values. Here is the example:
2ABC;t;t;t;tortuga;fault;t;t;bored
I want to replace them to '1' using sed.
If I make sed "s/;t;/;1;/g" I get the next result:
2ABC;1;t;1;tortuga;fault;1;t;bored
As you can see, consecutive ';t;' have been replaced through one. Yes, I can replace all ';t;' by sed -e "s/;t;/;1;/g" -e "s/;t;/;1;/g" but this is boring.
How can I make the replacement by one sed command?
If there is something to replace, branch to replace again.
sed ': again; /;t;/{ s//;1;/; b again }'
Overall, parsing cvs with sed is crude. Consider awk.
awk -F';' -v OFS=';' '{ for(i=1;i<=NF;++i) if ($i=="t") $i=1 } 1'
Lookarounds is helpful in such cases:
$ s='t;2ABC;t;t;t;tortuga;fault;t;t;bored;t'
$ echo "$s" | perl -lpe 's/(?<![^;])t(?![^;])/1/g'
1;2ABC;1;1;1;tortuga;fault;1;1;bored;1
echo '2ABC;t;t;t;tortuga;fault;t;t;bored' |
— gawk-specific solution
gawk -be '(ORS = RT)^!(NF = NF)' FS='^t$' OFS=1 RS=';'
— cross-awk-solution
{m,g,n}awk 'gsub(FS, OFS, $!(NF = NF))^_' FS=';t;' OFS=';1;' RS=
2ABC;1;1;1;tortuga;fault;1;1;bored
I have a file as below
NAME(BOLIVIA) TYPE(SA)
APPLIC(Java) IP(192.70.xxx.xx)
NAME(BOLIVIA) TYPE(SA)
APPLIC(Java) IP(192.71.xxx.xx)
I am trying to extract the values NAME and IP using sed:
cat file1 |
sed ':a
N
$!ba
s/\n/ /g' | sed -n 's/.*\(NAME(BOLI...)\).*\(IP(.*)\).*/\1 \2/p'
However, I'm only getting the output:
NAME(BOLIVIA) IP(192.71.xxx.xx)
What I would like is:
NAME(BOLIVIA) IP(192.70.xxx.xx)
NAME(BOLIVIA) IP(192.71.xxx.xx)
Would appreciate it if someone could give me a pointer on what I'm missing.
TIA
Your first sed commands reformats the file into one long line. You could have used tr -d "\n" for this, but that is not the problem.
The problem is in the second part, where the .* greedy eats as much as possible until finding the last match.
Your solution could be "fixed" with the ugly
# Do not use this:
sed -zn 's/[^\n]*\(NAME(BOLI...)\)[^\n]*\n[^\n]*\(IP([^)]*)\)[^\n]*/\1 \2/gp' file1
Possible solutions:
cat file1 | paste -d " " - - | sed -n 's/.*\(NAME(BOLI...)\).*\(IP(.*)\).*/\1 \2/p'
# or
grep -Eo "(NAME\(BOLI...\)|IP\(.*\))" file1 | paste -d " " - -
# or
printf "%s %s\n" $(grep -Eo "(NAME\(BOLI...\)|IP\(.*\))" file1)
In case you are ok with awk could you please try following. Written and tested in link
https://ideone.com/bJDzgf with shown samples only.
awk '
match($0,/^NAME\([^)]*/){
name=substr($0,RSTART+5,RLENGTH-5)
next
}
match($0,/IP\([^)]*/){
print name,substr($0,RSTART+3,RLENGTH-3)
name=""
}
' Input_file
This might work for you (GNU sed):
sed -n '/NAME/{N;/IP/s/\s.*\s/ /p}' file
If a line contains NAME and the following line contains IP remove everything between and print the result.
An alternative shorter awk:
awk '$1 ~ /^NAME/ {nm = $1} $2 ~ /^IP/ {print nm, $2}' file
NAME(BOLIVIA) IP(192.70.xxx.xx)
NAME(BOLIVIA) IP(192.71.xxx.xx)
The issue in your script is the use .* which matches in a greedy way
so that you have only the first NAME(BOLI...) and last IP(.*)
If you can use python :
#!/bin/bash
python -c '
import re, sys
for ar in re.findall(r"(NAME\(BOLI.*?\)).*?(IP\(.*?\))", sys.stdin.read(), re.DOTALL):
print(*ar)
' < input-file
I’m trying to replace the 3rd column of a file for itself plus the value of column 2 (without any space). I get the proper value for variable c and a but then sed doesn't give any output. Any clue?
#!/bin/tcsh
setenv c `cat lig_mod.pdb | awk '{print $3}'`
echo $c
setenv a `cat lig_mod.pdb | awk '{print $3=$3$2}'`
echo $a
sed -i "" 's/^'"${c}"'$/^'"${a}"'$/g' lig_mod.pdb
Even though awk is usually better for columns parsing this one-liner sed can work for you as well:
sed -i 's/ \(\w*\) \(\w*\) / \1 \2\1 /1' lig_mod.pdb
the '/1' at the end denote the instance number you desire to change which for the 2nd and 3rd columns is the first, but you could use it for any adjacent columns.
I have a line:
<random junk>TYPE=snp;<more random junk>
and I need to return everything between the end of TYPE= and the ; (in this case snp but it could be any of a number of text strings.
I tried various sed / awk solutions but I can't seem to get it working. I have the feeling this is a simple problem so, sorry about that.
This seems to work:
sed 's/.*TYPE=\(.*\);.*/\1/'
EDIT:
Ah, so there can be semicolons in the random junk. Try this:
sed 's/.*TYPE=\([^;]*\);.*/\1/'
requires GNU grep:
grep -Po '(?<=TYPE=)[^;]+'
meaning: preceded by "TYPE=", find some non-semicolon characters
One way using GNU sed:
sed -r 's/.*TYPE=([^;]+).*/\1/' file.txt
Since you also tagged this awk:
$ text='<random junk>TYPE=snp;<more random junk>'
$ echo "$text" | awk -FTYPE= '{sub(/;.*/,"",$2); print $2}'
snp
$ text='foo=bar;baz=fnu;TYPE=snp;XAI=0;XAM=0'
$ echo "$text" | awk -FTYPE= '{sub(/;.*/,"",$2); print $2}'
snp
(Only using the variable to keep the lines from wrapping.)
Or, to parse this as set of variable=value pairs rather than just a string of text:
$ echo "$text" | awk -vRS=";" -F= '$1=="TYPE" {print $2}'
snp
You can also do this in pure bash, if you want:
$ t="red=blue;TYPE=snp;XAI=0.0037843;XAM=0.0170293;XAS=0.013245;XRI=0;XRM=0"
$ t=${t#*TYPE=}
$ t=${t%%;*}
$ echo $t
snp
I have a text file looking like this:
(-9.1744438E-02,7.6282293E-02) (-9.1744438E-02,7.6282293E-02) ... and so on.
I would like to modify the file by removing all the parenthesis and a new line for each couple
so that it look like this:
-9.1744438E-02,7.6282293E-02
-9.1744438E-02,7.6282293E-02
...
A simple way to do that?
Any help is appreciated,
Fred
I would use tr for this job:
cat in_file | tr -d '()' > out_file
With the -d switch it just deletes any characters in the given set.
To add new lines you could pipe it through two trs:
cat in_file | tr -d '(' | tr ')' '\n' > out_file
As was said, almost:
sed 's/[()]//g' inputfile > outputfile
or in awk:
awk '{gsub(/[()]/,""); print;}' inputfile > outputfile
This would work -
awk -v FS="[()]" '{for (i=2;i<=NF;i+=2) print $i }' inputfile > outputfile
Test:
[jaypal:~/Temp] cat file
(-9.1744438E-02,7.6282293E-02) (-9.1744438E-02,7.6282293E-02)
[jaypal:~/Temp] awk -v FS="[()]" '{for (i=2;i<=NF;i+=2) print $i }' file
-9.1744438E-02,7.6282293E-02
-9.1744438E-02,7.6282293E-02
This might work for you:
echo "(-9.1744438E-02,7.6282293E-02) (-9.1744438E-02,7.6282293E-02)" |
sed 's/) (/\n/;s/[()]//g'
-9.1744438E-02,7.6282293E-02
-9.1744438E-02,7.6282293E-02
Guess we all know this, but just to emphasize:
Usage of bash commands is better in terms of time taken for execution, than using awk or sed to do the same job. For instance, try not to use sed/awk where grep can suffice.
In this particular case, I created a file 100000 lines long file, each containing characters "(" as well as ")". Then ran
$ /usr/bin/time -f%E -o log cat file | tr -d "()"
and again,
$ /usr/bin/time -f%E -ao log sed 's/[()]//g' file
And the results were:
05.44 sec : Using tr
05.57 sec : Using sed
cat in_file | sed 's/[()]//g' > out_file
Due to formatting issues, it is not entirely clear from your question whether you also need to insert newlines.