I'm a beginner in bash and here is my problem. I have a file just like this one:
Azzzezzzezzzezzz...
Bzzzezzzezzzezzz...
Czzzezzzezzzezzz...
I try in a script to edit this file.ABC letters are unique in all this file and there is only one per line.
I want to replace the first e of each line by a number who can be :
1 in line beginning with an A,
2 in line beginning with a B,
3 in line beginning with a C,
and I'd like to loop this in order to have this type of result
Azzz1zzz5zzz1zzz...
Bzzz2zzz4zzz5zzz...
Czzz3zzz6zzz3zzz...
All the numbers here are random int variables between 0 and 9. I really need to start by replacing 1,2,3 in first exec of my loop, then 5,4,6 then 1,5,3 and so on.
I tried this
sed "0,/e/s/e/$1/;0,/e/s/e/$2/;0,/e/s/e/$3/" /tmp/myfile
But the result was this (because I didn't specify the line)
Azzz1zzz2zzz3zzz...
Bzzzezzzezzzezzz...
Czzzezzzezzzezzz...
I noticed that doing sed -i "/A/ s/$/ezzz/" /tmp/myfile will add ezzz at the end of A line so I tried this
sed -i "/A/ 0,/e/s/e/$1/;/B/ 0,/e/s/e/$2/;/C/ 0,/e/s/e/$3/" /tmp/myfile
but it failed
sed: -e expression #1, char 5: unknown command: `0'
Here I'm lost.
I have in a variable (let's call it number_of_e_per_line) the number of e in either A, B or C line.
Thank you for the time you take for me.
Just apply s command on the line that matches A.
sed '
/^A/{ s/e/$1/; }
/^B/{ s/e/$2/; }
# or shorter
/^C/s/e/$3/
'
s command by default replaces the first occurrence. You can do for example s/s/$1/2 to replace the second occurrence, s/e/$1/g (like "Global") replaces all occurrences.
0,/e/ specifies a range of lines - it filters lines from the first up until a line that matches /e/.
sed is not part of Bash. It is a separate (crude) programming language and is a very standard command. See https://www.grymoire.com/Unix/Sed.html .
Continuing from the comment. sed is a poor choice here unless all your files can only have 3 lines. The reason is sed processes each line and has no way to keep a separate count for the occurrences of 'e'.
Instead, wrapping sed in a script and keeping track of the replacements allows you to handle any file no matter the number of lines. You just loop and handle the lines one at a time, e.g.
#!/bin/bash
[ -z "$1" ] && { ## valiate one argument for filename provided
printf "error: filename argument required.\nusage: %s filename\n" "./$1" >&2
exit 1
}
[ -s "$1" ] || { ## validate file exists and non-empty
printf "error: file not found or empty '%s'.\n" "$1"
exit 1
}
declare -i n=1 ## occurrence counter initialized 1
## loop reading each line
while read -r line || [ -n "$line" ]; do
[[ $line =~ ^.*e.*$ ]] || continue ## line has 'e' or get next
sed "s/e/1/$n" <<< "$line" ## substitute the 'n' occurence of 'e'
((n++)) ## increment counter
done < "$1"
Your data file having "..." at the end of each line suggests your files is larger than the snippet posted. If you have lines beginning 'A' - 'Z', you don't want to have to write 26 separate /match/s/find/replace/ substitutions. And if you have somewhere between 3 and 26 (or more), you don't want to have to rewrite a different sed expression for every new file you are faced with.
That's why I say sed is a poor choice. You really have no way to make the task a generic task with sed. The downside to using a script is it will become a poor choice as the number of records you need to process increase (over 100000 or so just due to efficiency)
Example Use/Output
With the script in replace-e-incremental.sh and your data in file, you would do:
$ bash replace-e-incremental.sh file
Azzz1zzzezzzezzz...
Bzzzezzz1zzzezzz...
Czzzezzzezzz1zzz...
To Modify file In-Place
Since you make multiple calls to sed here, you need to redirect the output of the file to a temporary file and then replace the original by overwriting it with the temp file, e.g.
$ bash replace-e-incremental.sh file > mytempfile && mv -f mytempfile file
$ cat file
Azzz1zzzezzzezzz...
Bzzzezzz1zzzezzz...
Czzzezzzezzz1zzz...
I am trying go count the length of each read in a fastq file from illumina sequencing and outputting this to a tsv or any sort of file so I can then later also look at this and count the number of reads per file. So I need to cycle down the file and eactract each line that has a read on it (every 4th line) then get its length and store this as an output
num=2
for file in *.fastq
do
echo "counting $file"
function file_length(){
wc -l $file | awk '{print$FNR}'
}
for line in $file_length
do
awk 'NR==$num' $file | chrlen > ${file}read_length.tsv
num=$((num + 4))
done
done
Currently all I get the counting $file and no other output but also no errors
Your script contains a lot of errors in both syntax and algorithm. Please try shellcheck to see what is the problem. The most issue will be the $file_length part.
You may want to call a function file_length() here but it is just
an undefined variable which is evaluated as null in the for loop.
If you just want to count the length of the 4th line of *.fastq files,
please try something like:
for file in *.fastq; do
awk 'NR==4 {print length}' "$file" > "${file}_length.tsv"
done
Or if you want to put the results together in a single tsv file, try:
tsvfile="read_lenth.tsv"
for file in *.fastq; do
echo -n -e "$file\t" >> "$tsvfile"
awk 'NR==4 {print length}' "$file" >> "$tsvfile"
done
Hope this helps.
I want to match the numbers in the first file with the 2nd column of second file and get the matching lines in a separate output file. Kindly let me know what is wrong with the code?
I have a list of numbers in a file IDS.txt
10028615
1003
10096344
10100
10107393
10113978
10163178
118747520
I have a second File called src1src22.txt
From src:'1' To src:'22'
CHEMBL3549542 118747520
CHEMBL548732 44526300
CHEMBL1189709 11740251
CHEMBL405440 44297517
CHEMBL310280 10335685
expected newoutput.txt
CHEMBL3549542 118747520
I have written this code
while read line; do cat src1src22.txt | grep -i -w "$line" >> newoutput.txt done<IDS.txt
Your command line works - except you're missing a semicolon:
while read line; do grep -i -w "$line" src1src22.txt; done < IDS.txt >> newoutput.txt
I have found an efficient way to perform the task. Instead of a loop try this -f gives the pattern in the file next to it and searches in the next file. The chance of invalid character length which can occur with grep is reduced and looping slows the process down.
grep -iw -f IDS.txt src1src22.tx >>newoutput.txt
Try this -
awk 'NR==FNR{a[$2]=$1;next} $1 in a{print a[$1],$0}' f2 f1
CHEMBL3549542 118747520
Where f2 is src1src22.txt
I wish to swap or transpose pairs of lines according to their line-numbers (e.g., switching the positions of lines 10 and 15) in multiple text files using a UNIX tool such as sed or awk.
For example, I believe this sed command should swap lines 14 and 26 in a single file:
sed -n '14p' infile_name > outfile_name
sed -n '26p' infile_name >> outfile_name
How can this be extended to work on multiple files? Any one-liner solutions welcome.
If you want to edit a file, you can use ed, the standard editor. Your task is rather easy in ed:
printf '%s\n' 14m26 26-m14- w q | ed -s file
How does it work?
14m26 tells ed to take line #14 and move it after line #26
26-m14- tells ed to take the line before line #26 (which is your original line #26) and move it after line preceding line #14 (which is where your line #14 originally was)
w tells ed to write the file
q tells ed to quit.
If your numbers are in a variable, you can do:
linea=14
lineb=26
{
printf '%dm%d\n' "$linea" "$lineb"
printf '%d-m%d-\n' "$lineb" "$linea"
printf '%s\n' w q
} | ed -s file
or something similar. Make sure that linea<lineb.
If you want robust in-place updating of your input files, use gniourf_gniourf's excellent ed-based answer
If you have GNU sed and want to in-place updating with multiple files at once, use
#potong's excellent GNU sed-based answer (see below for a portable alternative, and the bottom for an explanation)
Note: ed truly updates the existing file, whereas sed's -i option creates a temporary file behind the scenes, which then replaces the original - while typically not an issue, this can have undesired side effects, most notably, replacing a symlink with a regular file (by contrast, file permissions are correctly preserved).
Below are POSIX-compliant shell functions that wrap both answers.
Stdin/stdout processing, based on #potong's excellent answer:
POSIX sed doesn't support -i for in-place updating.
It also doesn't support using \n inside a character class, so [^\n] must be replaced with a cumbersome workaround that positively defines all character except \n that can occur on a line - this is a achieved with a character class combining printable characters with all (ASCII) control characters other than \n included as literals (via a command substitution using printf).
Also note the need to split the sed script into two -e options, because POSIX sed requires that a branching command (b, in this case) be terminated with either an actual newline or continuation in a separate -e option.
# SYNOPSIS
# swapLines lineNum1 lineNum2
swapLines() {
[ "$1" -ge 1 ] || { printf "ARGUMENT ERROR: Line numbers must be decimal integers >= 1.\n" >&2; return 2; }
[ "$1" -le "$2" ] || { printf "ARGUMENT ERROR: The first line number ($1) must be <= the second ($2).\n" >&2; return 2; }
sed -e "$1"','"$2"'!b' -e ''"$1"'h;'"$1"'!H;'"$2"'!d;x;s/^\([[:print:]'"$(printf '\001\002\003\004\005\006\007\010\011\013\014\015\016\017\020\021\022\023\024\025\026\027\030\031\032\033\034\035\036\037\177')"']*\)\(.*\n\)\(.*\)/\3\2\1/'
}
Example:
$ printf 'line 1\nline 2\nline 3\n' | swapLines 1 3
line 3
line 2
line 1
In-place updating, based on gniourf_gniourf's excellent answer:
Small caveats:
While ed is a POSIX utility, it doesn't come preinstalled on all platforms, notably not on Debian and the Cygwin and MSYS Unix-emulation environments for Windows.
ed always reads the input file as a whole into memory.
# SYNOPSIS
# swapFileLines lineNum1 lineNum2 file
swapFileLines() {
[ "$1" -ge 1 ] || { printf "ARGUMENT ERROR: Line numbers must be decimal integers >= 1.\n" >&2; return 2; }
[ "$1" -le "$2" ] || { printf "ARGUMENT ERROR: The first line number ($1) must be <= the second ($2).\n" >&2; return 2; }
ed -s "$3" <<EOF
H
$1m$2
$2-m$1-
w
EOF
}
Example:
$ printf 'line 1\nline 2\nline 3\n' > file
$ swapFileLines 1 3 file
$ cat file
line 3
line 2
line 1
An explanation of #potong's GNU sed-based answer:
His command swaps lines 10 and 15:
sed -ri '10,15!b;10h;10!H;15!d;x;s/^([^\n]*)(.*\n)(.*)/\3\2\1/' f1 f2 fn
-r activates support for extended regular expressions; here, notably, it allows use of unescaped parentheses to form capture groups.
-i specifies that the files specified as operands (f1, f2, fn) be updated in place, without backup, since no optional suffix for a backup file is adjoined to the -i option.
10,15!b means that all lines that do not (!) fall into the range of lines 10 through 15 should branch (b) implicitly to the end of the script (given that no target-label name follows b), which means that the following commands are skipped for these lines. Effectively, they are simply printed as is.
10h copies (h) line number 10 (the start of the range) to the so-called hold space, which is an auxiliary buffer.
10!H appends (H) every line that is not line 10 - which in this case implies lines 11 through 15 - to the hold space.
15!d deletes (d) every line that is not line 15 (here, lines 10 through 14) and branches to the end of the script (skips remaining commands). By deleting these lines, they are not printed.
x, which is executed only for line 15 (the end of the range), replaces the so-called pattern space with the contents of the hold space, which at that point holds all lines in the range (10 through 15); the pattern space is the buffer on which sed commands operate, and whose contents are printed by default (unless -n was specified).
s/^([^\n]*)(.*\n)(.*)/\3\2\1/ then uses capture groups (parenthesized subexpressions of the regular expression that forms the first argument passed to function s) to partition the contents of the pattern space into the 1st line (^([^\n]*)), the middle lines ((.*\n)), and the last line ((.*)), and then, in the replacement string (the second argument passed to function s), uses backreferences to place the last line (\3) before the middle lines (\2), followed by the first line (\1), effectively swapping the first and last lines in the range. Finally, the modified pattern space is printed.
As you can see, only the range of lines spanning the two lines to swap is held in memory, whereas all other lines are passed through individually, which makes this approach memory-efficient.
This might work for you (GNU sed):
sed -ri '10,15!b;10h;10!H;15!d;x;s/^([^\n]*)(.*\n)(.*)/\3\2\1/' f1 f2 fn
This stores a range of lines in the hold space and then swaps the first and last lines following the completion of the range.
The i flag edits each file (f1,f2 ... fn) in place.
With GNU awk:
awk '
FNR==NR {if(FNR==14) x=$0;if(FNR==26) y=$0;next}
FNR==14 {$0=y} FNR==26 {$0=x} {print}
' file file > file_with_swap
The use of the following helper script allows using the power of find ... -exec ./script '{}' l1 l2 \; to locate the target files and to swap lines l1 & l2 in each file in place. (it requires that there are no identical duplicate lines within the file that fall within the search range) The script uses sed to read the two swap lines from each file into an indexed array and passes the lines to sed to complete the swap by matching. The sed call uses its "matched first address" state to limit the second expression swap to the first occurrence. An example use of the helper script below to swap lines 5 & 15 in all matching files is:
find . -maxdepth 1 -type f -name "lnum*" -exec ../swaplines.sh '{}' 5 15 \;
For example, the find call above found files lnumorig.txt and lnumfile.txt in the present directory originally containing:
$ head -n20 lnumfile.txt.bak
1 A simple line of test in a text file.
2 A simple line of test in a text file.
3 A simple line of test in a text file.
4 A simple line of test in a text file.
5 A simple line of test in a text file.
6 A simple line of test in a text file.
<snip>
14 A simple line of test in a text file.
15 A simple line of test in a text file.
16 A simple line of test in a text file.
17 A simple line of test in a text file.
18 A simple line of test in a text file.
19 A simple line of test in a text file.
20 A simple line of test in a text file.
And swapped the lines 5 & 15 as intended:
$ head -n20 lnumfile.txt
1 A simple line of test in a text file.
2 A simple line of test in a text file.
3 A simple line of test in a text file.
4 A simple line of test in a text file.
15 A simple line of test in a text file.
6 A simple line of test in a text file.
<snip>
14 A simple line of test in a text file.
5 A simple line of test in a text file.
16 A simple line of test in a text file.
17 A simple line of test in a text file.
18 A simple line of test in a text file.
19 A simple line of test in a text file.
20 A simple line of test in a text file.
The helper script itself is:
#!/bin/bash
[ -z $1 ] && { # validate requierd input (defaults set below)
printf "error: insufficient input calling '%s'. usage: file [line1 line2]\n" "${0//*\//}" 1>&2
exit 1
}
l1=${2:-10} # default/initialize line numbers to swap
l2=${3:-15}
while IFS=$'\n' read -r line; do # read lines to swap into indexed array
a+=( "$line" );
done <<<"$(sed -n $((l1))p "$1" && sed -n $((l2))p "$1")"
((${#a[#]} < 2)) && { # validate 2 lines read
printf "error: requested lines '%d & %d' not found in file '%s'\n" $l1 $l2 "$1"
exit 1
}
# swap lines in place with sed (remove .bak for no backups)
sed -i.bak -e "s/${a[1]}/${a[0]}/" -e "0,/${a[0]}/s/${a[0]}/${a[1]}/" "$1"
exit 0
Even though I didn't manage to get it all done in a one-liner I decided it was worth posting in case you can make some use of it or take ideas from it. Note: if you do make use of it, test to your satisfaction before turning it loose on your system. The script currently uses sed -i.bak ... to create backups of the files changed for testing purposes. You can remove the .bak when you are satisfied it meets your needs.
If you have no use for setting default lines to swap in the helper script itself, then I would change the first validation check to [ -z $1 -o -z $2 -o $3 ] to insure all required arguments are given when the script is called.
While it does identify the lines to be swapped by number, it relies on the direct match of each line to accomplish the swap. This means that any identical duplicate lines up to the end of the swap range will cause an unintended match and failue to swap the intended lines. This is part of the limitation imposed by not storing each line within the range of lines to be swapped as discussed in the comments. It's a tradeoff. There are many, many ways to approach this, all will have their benefits and drawbacks. Let me know if you have any questions.
Brute Force Method
Per your comment, I revised the helper script to use the brute forth copy/swap method that would eliminate the problem of any duplicate lines in the search range. This helper obtains the lines via sed as in the original, but then reads all lines from file to tmpfile swapping the appropriately numbered lines when encountered. After the tmpfile is filled, it is copied to the original file and tmpfile is removed.
#!/bin/bash
[ -z $1 ] && { # validate requierd input (defaults set below)
printf "error: insufficient input calling '%s'. usage: file [line1 line2]\n" "${0//*\//}" 1>&2
exit 1
}
l1=${2:-10} # default/initialize line numbers to swap
l2=${3:-15}
while IFS=$'\n' read -r line; do # read lines to swap into indexed array
a+=( "$line" );
done <<<"$(sed -n $((l1))p "$1" && sed -n $((l2))p "$1")"
((${#a[#]} < 2)) && { # validate 2 lines read
printf "error: requested lines '%d & %d' not found in file '%s'\n" $l1 $l2 "$1"
exit 1
}
# create tmpfile, set trap, truncate
fn="$1"
rmtemp () { cp "$tmpfn" "$fn"; rm -f "$tmpfn"; }
trap rmtemp SIGTERM SIGINT EXIT
declare -i n=1
tmpfn="$(mktemp swap_XXX)"
:> "$tmpfn"
# swap lines in place with a tmpfile
while IFS=$'\n' read -r line; do
if ((n == l1)); then
printf "%s\n" "${a[1]}" >> "$tmpfn"
elif ((n == l2)); then
printf "%s\n" "${a[0]}" >> "$tmpfn"
else
printf "%s\n" "$line" >> "$tmpfn"
fi
((n++))
done < "$fn"
exit 0
If the line numbers to be swapped are fixed then you might want to try something like the sed command in the following example to have lines swapped in multiple files in-place:
#!/bin/bash
# prep test files
for f in a b c ; do
( for i in {1..30} ; do echo $f$i ; done ) > /tmp/$f
done
sed -i -s -e '14 {h;d}' -e '15 {N;N;N;N;N;N;N;N;N;N;G;x;d}' -e '26 G' /tmp/{a,b,c}
# -i: inplace editing
# -s: treat each input file separately
# 14 {h;d} # first swap line: hold ; suppress
# 15 {N;N;...;G;x;d} # lines between: collect, append held line; hold result; suppress
# 26 G # second swap line: append held lines (and output them all)
# dump test files
cat /tmp/{a,b,c}
(This is according to Etan Reisner's comment.)
If you want to swap two lines, you can send it through twice, you could make it loop in one sed script if you really wanted, but this works:
e.g.
test.txt: for a in {1..10}; do echo "this is line $a"; done >> test.txt
this is line 1
this is line 2
this is line 3
this is line 4
this is line 5
this is line 6
this is line 7
this is line 8
this is line 9
this is line 10
Then to swap lines 6 and 9:
sed ':a;6,8{6h;6!H;d;ba};9{p;x};' test.txt | sed '7{h;d};9{p;x}'
this is line 1
this is line 2
this is line 3
this is line 4
this is line 5
this is line 9
this is line 7
this is line 8
this is line 6
this is line 10
In the first sed it builds up the hold space with lines 6 through 8.
At line 9 it prints line 9 then prints the hold space (lines 6 through 8) this accomplishes the first move of 9 to place 6. Note: 6h; 6!H avoids a new line at the top of the pattern space.
The second move occurs in the second sed script it saves line 7 to the hold space, then deletes it and prints it after line 9.
To make it quasi-generic you can use variables like this:
A=3 && B=7 && sed ':a;'${A}','$((${B}-1))'{'${A}'h;'${A}'!H;d;ba};'${B}'{p;x};' test.txt | sed $(($A+1))'{h;d};'${B}'{p;x}'
Where A and B are the lines you want to swap, in this case lines 3 and 7.
if, you want swap two lines, to create script "swap.sh"
#!/bin/sh
sed -n "1,$((${2}-1))p" "$1"
sed -n "${3}p" "$1"
sed -n "$((${2}+1)),$((${3}-1))p" "$1"
sed -n "${2}p" "$1"
sed -n "$((${3}+1)),\$p" "$1"
next
sh swap.sh infile_name 14 26 > outfile_name
I am trying to append an index variable at the end of each line of a file that I have. However I dont want to lose the escape characters that I have in the textFile and thus cannot echo into the file again.
Here's what I tried:
while read p; do
tempCom+=$p
tempCom+=$indexVar
echo $tempCom >> otherFile.txt
tempCom=""
done < result.txt
What I am after:
Read:
"asdasdasdasdasdasd\ asdasd/asda"
"qweqweqweqweqweqwe\ qweqwe/qweq"
Output:
"asdasdasdasdasdasd\ asdasd/asda" 1
"qweqweqweqweqweqwe\ qweqwe/qweq" 2
Note that indexVar is an index that is stored elsewhere and does not necessarily correspond to the line that its being appended to.
Your problem is very likely a quoting problem. Observe the IFS= and the -r option in the read statement too.
while IFS= read -r p
tempCom+=$p$indexVar
printf '%s\n' "$tempCom" >> otherFile.txt # Observe the quotes
tempCom=
done < result.txt
If you just want to append the line number to the end why not use awk?
awk '{print $0, "\t", NR}' < file.txt
EDIT 1: It sounds like you want to use paste then (assuming you want to just join line by line)
paste file1.txt file2.txt > fileresults.txt
EDIT 2: You can use sed then:
sed "s|$|${indexVar}|" input
Use the -r option of the read command, so that the backslashes are preserved.
while read -r p; do