I am trying to replace every 4th occurrence of "_" with "#" in multiple files with bash.
E.g.
foo_foo_foo_foo_foo_foo_foo_foo_foo_foo..
would become
foo_foo_foo_foo#foo_foo_foo_foo#foo_foo...
#perl -pe 's{_}{++$n % 4 ? $& : "#"}ge' *.txt
I have tried perl but the problem is this replaces every 4th _ carrying on from the last file. So for example, some files the first _ is replaced because it is not starting each new file at a count of 0, it carries on from the previous file.
I have tried:
#awk '{for(i=1; i<=NF; i++) if($i=="_") if(++count%4==0) $i="#"}1' *.txt
but this also does not work.
Using sed I cannot find a way to keep replacing every 4th occurrence as there are different numbers of _ in each file. Some files have 20 _, some have 200 _. Therefore, I cant specify a range.
I am really lost what to do, can anybody help?
You just need to reset the counter in the perl one using eof to tell when it's done reading each file:
perl -pe 's{_}{++$n % 4 ? "_" : "#"}ge; $n = 0 if eof' *.txt
This MAY be what you want, using GNU awk for RT:
$ awk -v RS='_' '{ORS=(FNR%4 ? RT : "#")} 1' file
foo_foo_foo_foo#foo_foo_foo_foo#foo_foo..
It only reads each _-separated string into memory 1 at a time so should work no matter how large your input file, assuming there are _s in it.
It assumes you want to replace every 4th _ across the whole file as opposed to within individual lines.
A simple sed would handle this:
s='foo_foo_foo_foo_foo_foo_foo_foo_foo_foo'
sed -E 's/(([^_]+_){3}[^_]+)_/\1#/g' <<< "$s"
foo_foo_foo_foo#foo_foo_foo_foo#foo_foo
Explanation:
(: Start capture group #1
([^_]+_){3}: Match Match 1+ of non-_ characters followed by a _. Repeat this group 3 times to match 3 such words separated by _
[^_]+: Match 1+ of non-_ characters
): End capture group #1
_: Match a _
Replacement is \1# to replace 4th _ with a #
With GNU sed:
sed -nsE ':a;${s/(([^_]*_){3}[^_]*)_/\1#/g;p};N;ba' *.txt
-n suppresses the automatic printing, -s processes each file separately, -E uses extended regular expressions.
The script is a loop between label a (:a) and the branch-to-label-a command (ba). Each iteration appends the next line of input to the pattern space (N). This way, after the last line has been read, the pattern space contains the whole file(*). During the last iteration, when the last line has been read ($), a substitute command (s) replaces every 4th _ in the pattern space by a # (s/(([^_]*_){3}[^_]*)_/\1#/g) and prints (p) the result.
When you will be satisfied with the result you can change the options:
sed -i -nE ':a;${s/(([^_]*_){3}[^_]*)_/\1#/g;p};N;ba' *.txt
to modify the files in-place, or:
sed -i.bkp -nE ':a;${s/(([^_]*_){3}[^_]*)_/\1#/g;p};N;ba' *.txt
to modify the files in-place, but keep a *.txt.bkp backup of each file.
(*) Note that if you have very large files this could cause memory overflows.
With your shown samples, please try following awk program. Have created an awk variable named fieldNum where I have assigned 4 to it, since OP needs to enter # after every 4th _, you can keep it as per your need too.
awk -v fieldNum="4" '
BEGIN{ FS=OFS="_" }
{
val=""
for(i=1;i<=NF;i++){
val=(val?val:"") $i (i%fieldNum==0?"#":(i<NF?OFS:""))
}
print val
}
' Input_file
With GNU awk
$ cat ip.txt
foo_foo_foo_foo_foo_foo_foo_foo_foo_foo
123_45678_90
_
$ awk -v RS='(_[^_]+){3}_' -v ORS= '{sub(/_$/, "#", RT); print $0 RT}' ip.txt
foo_foo_foo_foo#foo_foo_foo_foo#foo_foo
123_45678_90
#
-v RS='(_[^_]+){3}_' set input record separator to cover sequence of four _ (text matched by this separator will be available via RT)
-v ORS= empty output record separator
sub(/_$/, "#", RT) change last _ to #
Use -i inplace for inplace editing.
If the count should reset for each line:
perl -pe's/(?:_[^_]*){3}\K_/\#/g'
$ cat a.txt
foo_foo_foo_foo_foo_foo_foo_foo_foo_foo
foo_foo_foo_foo_foo_foo_foo_foo_foo_foo
$ perl -pe's/(?:_[^_]*){3}\K_/\#/g' a.txt a.txt
foo_foo_foo_foo#foo_foo_foo_foo#foo_foo
foo_foo_foo_foo#foo_foo_foo_foo#foo_foo
foo_foo_foo_foo#foo_foo_foo_foo#foo_foo
foo_foo_foo_foo#foo_foo_foo_foo#foo_foo
If the count shouldn't reset for each line, but should reset for each file:
perl -0777pe's/(?:_[^_]*){3}\K_/\#/g'
The -0777 cause the whole file to be treated as one line. This causes the count to work properly across lines.
But since a new a match is used for each file, the count is reset between files.
$ cat a.txt
foo_foo_foo_foo_foo_foo_foo_foo_foo_foo
foo_foo_foo_foo_foo_foo_foo_foo_foo_foo
$ perl -0777pe's/(?:_[^_]*){3}\K_/\#/g' a.txt a.txt
foo_foo_foo_foo#foo_foo_foo_foo#foo_foo
foo_foo_foo#foo_foo_foo_foo#foo_foo_foo
foo_foo_foo_foo#foo_foo_foo_foo#foo_foo
foo_foo_foo#foo_foo_foo_foo#foo_foo_foo
To avoid that reading the entire file at once, you could continue using the same approach, but with the following added:
$n = 0 if eof;
Note that eof is not the same thing as eof()! See eof.
Related
I am trying to change long names in rows starting with >, so that I only keep the part till Stage_V_sporulation_protein...:
>tr_A0A024P1W8_A0A024P1W8_9BACI_Stage_V_sporulation_protein_AE_OS=Halobacillus_karajensis_OX=195088_GN=BN983_00096_PE=4_SV=1
MTFLWAFLVGGGICVIGQILLDVFKLTPAHVMSSFVVAGAVLDAFDLYDNLIRFAGGGATVPITSFGHSLLHGAMEQADEHGVIGVAIGIFELTSAGIASAILFGFIVAVIFKPKG
>tr_A0A060LWV2_A0A060LWV2_9BACI_SpoIVAD_sporulation_protein_AEB_OS=Alkalihalobacillus_lehensis_G1_OX=1246626_GN=BleG1_2089_PE=4_SV=1
MIFLWAFLVGGVICVIGQLLMDVVKLTPAHTMSTLVVSGAVLAGFGLYEPLVDFAGAGATVPITSFGNSLVQGAMEEANQVGLIGIITGIFEITSAGISAAIIFGFIAALIFKPKG
I am doing a loop:
cat file.txt | while read line; do
if [[ $line = \>* ]] ; then
cut -d_ -f1-4 $line;
fi;
done
but in addresses files but not rows in the file (I get cut: >>tr_A0A024P1W8_A0A024P1W8_9BACI_Stage_V_sporulation_protein_AE_OS=Halobacillus_karajensis_OX=195088_GN=BN983_00096_PE=4_SV=1: No such file or directory).
My desired output is:
>tr_A0A024P1W8_A0A024P1W8_9BACI
MTFLWAFLVGGGICVIGQILLDVFKLTPAHVMSSFVVAGAVLDAFDLYDNLIRFAGGGATVPITSFGHSLLHGAMEQADEHGVIGVAIGIFELTSAGIASAILFGFIVAVIFKPKG
>tr_A0A060LWV2_A0A060LWV2_9BACI
MIFLWAFLVGGVICVIGQLLMDVVKLTPAHTMSTLVVSGAVLAGFGLYEPLVDFAGAGATVPITSFGNSLVQGAMEEANQVGLIGIITGIFEITSAGISAAIIFGFIAALIFKPKG
How do I change actual rows?
With the current state of the question, it seems easiest to do:
awk '/^>/ {print $1,$2,$3,$4; next}1' FS=_ OFS=_ file.txt
Lines that match the > at the beginning of the line get only the first four fields printed, separated by _ (the value of OFS). Lines that do not match are printing unchanged.
One way using sed:
sed -E '/^>/s/(.*)_Stage_V_sporulation_protein/\1/' file
A sed one-liner would be:
sed '/^>/s/^\(\([^_]*_\)\{3\}[^_]*\).*/\1/' file
Use this Perl one-liner to process the headers in your FASTA file:
perl -lpe 'if ( m{^>} ) { #f = split m{_}, $_; splice #f, 4; $_ = join "_", #f; }' file.txt > out.txt
The Perl one-liner uses these command line flags:
-e : Tells Perl to look for code in-line, instead of in a file.
-p : Loop over the input one line at a time, assigning it to $_ by default. Add print $_ after each loop iteration.
-l : Strip the input line separator ("\n" on *NIX by default) before executing the code in-line, and append it when printing.
The one-liner uses split to split the input string on underscore into the array #f.
Then splice is used to remove from the array all elements except for the first 4 elements.
Finally, join joins these elements on an underscore.
All of the above is wrapped inside if ( m{^>} ) { ... } in order to limit the costly string manipulations only to the FASTA headers (the lines that start with >).
SEE ALSO:
perldoc perlrun: how to execute the Perl interpreter: command line switches
Using bash how do I find a string and update the string next to it for example pass value
my.site.com|test2.spin:80
proxy_pass.map
my.site2.com test2.spin:80
my.site.com test.spin:8080;
Expected output is to update proxy_pass.map with
my.site2.com test2.spin:80
my.site.com test2.spin:80;
I tried using awk
awk '{gsub(/^my\.site\.com\s+[A-Za-z0-9]+\.spin:8080;$/,"my.site2.comtest2.spin:80"); print}' proxy_pass.map
but does not seem to work. Is there a better way to approch the problem. ?
One awk idea, assuming spacing needs to be maintained:
awk -v rep='my.site.com|test2.spin:80' '
BEGIN { split(rep,a,"|") # split "rep" variable and store in
site[a[1]]=a[2] # associative array
}
$1 in site { line=$0 # if 1st field is in site[] array then make copy of current line
match(line,$1) # find where 1st field starts (in case 1st field does not start in column #1)
newline=substr(line,1,RSTART+RLENGTH-1) # save current line up through matching 1st field
line=substr(line,RSTART+RLENGTH) # strip off 1st field
match(line,/[^[:space:];]+/) # look for string that does not contain spaces or ";" and perform replacement, making sure to save everything after the match (";" in this case)
newline=newline substr(line,1,RSTART-1) site[$1] substr(line,RSTART+RLENGTH)
$0=newline # replace current line with newline
}
1 # print current line
' proxy_pass.map
This generates:
my.site2.com test2.spin:80
my.site.com test2.spin:80;
If the input looks like:
$ cat proxy_pass.map
my.site2.com test2.spin:80
my.site.com test.spin:8080;
This awk script generates:
my.site2.com test2.spin:80
my.site.com test2.spin:80;
NOTES:
if multiple replacements need to be performed I'd suggest placing them in a file and having awk process said file first
the 2nd match() is hardcoded based on OP's example; depending on actual file contents it may be necessary to expand on the regex used in the 2nd match()
once satisified with the result the original input file can be updated in a couple ways ... a) if using GNU awk then awk -i inplace -v rep.... or b) save result to a temp file and then mv the temp file to proxy_pass.map
If the number of spaces between the columns is not significant, a simple
proxyf=proxy_pass.map
tmpf=$$.txt
awk '$1 == "my.site.com" { $2 = "test2.spin:80;" } {print}' <$proxyf >$tmpf && mv $tmpf $proxyf
should do. If you need the columns to be lined up nicely, you can replace the print by a suitable printf .... statement.
With your shown samples and attempts please try following awk code. Creating shell variable named var where it stores value my.site.com|test2.spin:80 in it. which further is being passed to awk program. In awk program creating variable named var1 which has shell variable var's value in it.
In BEGIN section of awk using split function to split value of var(shell variable's value container) into array named arr with separator as |. Where num is total number of values delimited by split function. Then using for loop to be running till value of num where it creates array named arr2 with index of current i value and making i+1 as its value(basically 1 is for key of array and next item is value of array).
In main block of awk program checking condition if $1 is in arr2 then print arr2's value else print $2 value as per requirement.
##Shell variable named var is being created here...
var="my.site.com|test2.spin:80"
awk -v var1="$var" '
BEGIN{
num=split(var1,arr,"|")
for(i=1;i<=num;i+=2){
arr2[arr[i]]=arr[i+1]
}
}
{
print $1,(($1 in arr2)?arr2[$1]:$2)
}
' Input_file
OR in case you want to maintain spaces between 1st and 2nd field(s) then try following code little tweak of Above code. Written and tested with your shown samples Only.
awk -v var1="$var" '
BEGIN{
num=split(var1,arr,"|")
for(i=1;i<=num;i+=2){
arr2[arr[i]]=arr[i+1]
}
}
{
match($0,/[[:space:]]+/)
print $1 substr($0,RSTART,RLENGTH) (($1 in arr2)?arr2[$1]:$2)
}
' Input_file
NOTE: This program can take multiple values separated by | in shell variable to be passed and checked on in awk program. But it considers that it will be in format of key|value|key|value... only.
#!/bin/sh -x
f1=$(echo "my.site.com|test2.spin:80" | cut -d'|' -f1)
f2=$(echo "my.site.com|test2.spin:80" | cut -d'|' -f2)
echo "${f1}%${f2};" >> proxy_pass.map
tr '%' '\t' < proxy_pass.map >> p1
cat > ed1 <<EOF
$
-1
d
wq
EOF
ed -s p1 < ed1
mv -v p1 proxy_pass.map
rm -v ed1
This might work for you (GNU sed):
<<<'my.site.com|test2.spin:80' sed -E 's#\.#\\.#g;s#^(\S+)\|(\S+)#/^\1\\b/s/\\S+/\2/2#' |
sed -Ef - file
Build a sed script from the input arguments and apply it to the input file.
The input arguments are first prepared so that their metacharacters ( in this case the .'s are escaped.
Then the first argument is used to prepare a match command and the second is used as the value to be replaced in a substitution command.
The result is piped into a second sed invocation that takes the sed script and applies it the input file.
with input csv file
sid,storeNo,latitude,longitude
2,1,-28.03720000,153.42921670
9
I wish to output only the lines with one column, in this example it's line 3.
how can this be done in bash shell script?
Using awk
The following awk would be usfull
$ awk -F, 'NF==1' inputFile
9
What it does?
-F, sets the field separator as ,
NF==1 matches lines with NF, number of fields as 1. No action is provided hence default action, printing the entire record is taken. it is similar to NF==1{print $0}
inputFile input csv file to the awk script
Using grep
The same function can also be done using grep
$ grep -v ',' inputFile
9
-v option prints lines that do not match the pattern
, along with -v greps matches lines that do not contain , field separator
Using sed
$ sed -n '/^[^,]*$/p' inputFile
9
what it does?
-n suppresses normal printing of pattern space
'/^[^,]*$/ selects lines that match the pattern, lines without any ,
^ anchors the regex at the start of the string
[^,]* matches anything other than ,
$ anchors string at the end of string
p action p makes sed to print the current pattern space, that is pattern space matching the input
try this bash script
#!/bin/bash
while read -r line
do
IFS=","
set -- $line
case ${#} in
1) echo $line;;
*) continue;;
esac
done < file
I have a file with contents
x
a
x
b
x
c
I want to grep the last occurrence,
x
c
when I try
sed -n "/x/,/b/p" file
it lists all the lines, beginning x to c.
I'm not sure if I got your question right, so here are some shots in the dark:
Print last occurence of x (regex):
grep x file | tail -1
Alternatively:
tac file | grep -m1 x
Print file from first matching line to end:
awk '/x/{flag = 1}; flag' file
Print file from last matching line to end (prints all lines in case of no match):
tac file | awk '!flag; /x/{flag = 1};' | tac
grep -A 1 x file | tail -n 2
-A 1 tells grep to print one line after a match line
with tail you get the last two lines.
or in a reversed way:
tac fail | grep -B 1 x -m1 | tac
Note: You should make sure your pattern is "strong" enough so it gets you the right lines. i.e. by enclosing it with ^ at the start and $ at the end.
This might work for you (GNU sed):
sed 'H;/x/h;$!d;x' file
Saves the last x and what follows in the hold space and prints it out at end-of-file.
not sure how to do it using sed, but you can try awk
awk '{a=a"\n"$0; if ($0 == "x"){ a=$0}} END{print a}' file
POSIX vi (or ex or ed), in case it is useful to someone
Done in Command mode, of course
:set wrapscan
Go to the first line and just search Backwards!
1G?pattern
Slower way, without :set wrapscan
G$?pattern
Explanation:
G go to the last line
Move to the end of that line $
? search Backwards for pattern
The first backwards match will be the same as the last forward match
Either way, you may now delete all lines above current (match)
:1,.-1d
or
kd1G
You could also delete to the beginning of the matched line prior to the line deletions with d0 in case there were multiple matches on the same line.
POSIX awk, as suggested at
get last line from grep search on multiple files
awk '(FNR==1)&&s{print s; s=""}/PATTERN/{s=$0}END{if(s) print s}'
if you wanna do awk in truly hideous one-liner fashion but getting awk to resemble closer to functional programming paradigm syntax without having to keep track when the last occurrence is
mawk/mawk2/gawk 'BEGIN { FS = "=7713[0-9]+="; RS = "^$";
} END { print ar0[split($(0 * sub(/\n.+$/,"",$NF)), ar0, ORS)] }'
Here i'm employing multiple awk short-hands :
sub(/[\n.+$/, "", $NF) # trimming all extra rows after pattern
g/sub() returns # of substitutions made, so multiplying that by 0 forces the split() to be splitting $0, the full file, instead.
split() returns # of items in the array (which is another way of saying the position of last element), so even though I've already trimmed out the trailing \n, i still can directly print ar0[split()], knowing that ORS will fill in the missing trailing \n.
That's why this code looks like i'm trying to extract array items before the array itself is defined, but due to flow of logic needed, the array will become defined by the time it reaches print.
Now if you want something simpler, these 2 also work
mawk/gawk 'BEGIN { FS="=7713[0-9]+="; RS = "^$"
} END { $NF = substr($NF, 1, index($NF, ORS));
FS = ORS; $0 = $0; print $(NF-1) }'
or
mawk/gawk '/=7713[0-9]+=/ { lst = $0 } END { print lst }'
I didn't use the same x|c requirements as OP just to showcase these work regardless of whether you need fixed-strings or regex based matches.
The above solutions only work for one single file, to print the last occurrence for many files (say with suffix .txt), use the following bash script
#!/bin/bash
for fn in `ls *.txt`
do
result=`grep 'pattern' $fn | tail -n 1`
echo $result
done
where 'pattern' is what you would like to grep.
I am using sed to find a certain match in a text file and then put this value in to a variable, my problem is that I only want the text after the match, and not the entire line.
Ans=$(sed -n '/^'$1':/,/~/{/:/{p;n};/~/q;p}' $file.txt)
Text File
q1:answer1
~
q2:answer2
~
q3:answer3
~
Actual Output
q1:answer1
Expected Output
answer1
With grep :
Ans=$(grep -oP "^$1:\K.*" file)
or with perl if your grep version doesn't support -P switch :
Ans=$(var=$1 perl -lne '/^$ENV{var}:\K.*/ and print $&' file)
In case a sed solution is needed - e.g., if answers could span multiple lines:
Ans=$(sed -r -n '/^'$1':(.*)/,/^(~)$/ { s//\1/; /^~$/q; p; }' file.txt)
(OSX users: use -E instead of -r).
Uses a backreference (\1) to replace the first matching line with its portion of interest; any other lines between the first matching one and the terminating ~ line are unaffected by the replacement (assuming they don't also start with $1:) and also printed.
Replace q with d if you don't want to quit after the first matching range.
By contrast, if the string of interest is limited to the line starting with $1:, there's no need to also match the ~ line, and the command can be simplified to:
Ans=$(sed -r -n '/^'$1':(.*)/ { s//\1/p; q; }' file.txt)
Remove q; if you don't want to quit after the first match.
However, the single-line case is more easily handled with a grep or awk solution - see #sputnick's and #anubhava's answers. If you wanted those to quit after the first match -- as in the snippets above and the code in the OP -- you'd need to add option -m 1 to the grep solution and ; exit to the awk solution (before the }).
Better use awk for this:
ans=$(awk -F':' -v s='q1' '$1 == s {print $2}' file)