Pipe awk's results to sed (deletion) - regex

I am using an awk command (someawkcommand) that prints these lines (awkoutput):
>Genome1
ATGCAAAAG
CAATAA
and then, I want to use this output (awkoutput) as the input of a sed command. Something like that:
someawkcommand | sed 's/awkoutput//g' file1.txt > results.txt
file1.txt:
>Genome1
ATGCAAAAG
CAATAA
>Genome2
ATGAAAAA
AAAAAAAA
CAA
>Genome3
ACCC
The final objective is to delete all lines in a file (file1.txt) containing the exact pattern found previously by awk.
The file results.txt contains (output of sed):
>Genome2
ATGAAAAA
AAAAAAAA
CAA
>Genome3
ACCC
How should I write the sed command? Is there any simple way that sed will recognize the output of awk as its input?

Using GNU awk for multi-char RS:
$ cat file1
>Genome1
ATGCAAAAG
CAATAA
$ cat file2
>Genome1
ATGCAAAAG
CAATAA
>Genome2
ATGAAAAA
AAAAAAAA
CAA
>Genome3
ACCC
$ gawk -v RS='^$' -v ORS= 'NR==FNR{rmv=$0;next} {sub(rmv,"")} 1' file1 file2
>Genome2
ATGAAAAA
AAAAAAAA
CAA
>Genome3
ACCC
The stuff that might be non-obvious to newcomers but are very common awk idioms:
-v RS='^$' tells awk to read the whole file as one string (instead of it's default one line at a time).
-v ORS= sets the Output Record Separator to the null string (instead of it's default newline) so that when the file is printed as a string awk doesn't add a newline after it.
NR==FNR is a condition that is only true for the first input file.
1 is a true condition invoking the default action of printing the current record.

Here is a possible sed solution:
someawkcommand | sed -n 's_.*_/&/d;_;H;${x;s_\n__g p}' | sed -f - file1.txt
First sed command turns output from someawkcommand into a sed expression.
Concretely, it turns
>Genome1
ATGCAAAAG
CAATAA
into:
/>Genome1/d;/ATGCAAAAG/d;/CAATAA/d;
(in sed language: delete lines containing those patterns; mind that you will have to escape /,[,],*,^,$ in your awk output if there are some, with another substitution for instance).
Second sed command reads it as input expression (-f - reads sed commands from file -, i.e. gets it from pipe) and applies to file file1.txt.
Remark for other readers:
OP wants to use sed, but as notified in comments, it may not be the easiest way to solve this question. Deleting lines with awk could be simpler. Another (easy) solution could be to use grep with -v (invert match) and -f (read patterns from files) options, in this way:
someawkcommand | grep -v -f - file1.txt
Edit: Following #rici's comments, here is a new command that takes output from awk as a single multiline pattern.
Disclaimer: It gets dirty. Kids, don't do it home. Grown-ups are strongly encouraged to consider avoiding sed for that.
someawkcommand | \
sed -n 'H;${x;s_\n__;s_\n_\\n_g;s_.*_H;${x;s/\\n//;s/&//g p}_ p}' | \
sed -n -f - file1.txt
Output from inner sed is:
H;${x;s/\n//;s/>Genome1\nATGCAAAAG\nCAATAA//g p}
Additional drawback: it will add an empty line instead of removed pattern. Can't fix it easily (problems if pattern is at beginning/end of file). Add a substitution to remove it if you really feel like it.

This is can more easily be done in awk, but the usual "eliminate duplicates" code is not correct. As I understand the question, the goal is to remove entire stanzas from the file.
Here's a possible solution which assumes that the first awk script outputs a single stanza:
awk 'NR == FNR {stanza[nstanza++] = $0; next}
$0 == stanza[i] {++i; next}
/^>/ && i == nstanza {i=0; next}
i {for (j=0; j<i; ++j) print stanza[j]; i=0}
{print $0;}
' <(someawkcommand) file1.txt

This might work for you (GNU sed):
sed '1{h;s/.*/:a;$!{N;ba}/p;d};/^>/!{H;$!d};x;s/\n/\\n/g;s|.*|s/&\\n*//g|p;$s|.*|s/\\n*$//|p;x;h;d' file1
sed -f - file2
This builds a script from file1 and then runs it against file2.
The script slurps in file2 and then does a gobal substitution(s) using the contents of file1. Finally it removes any blank lines at the end file caused by the contents deletion.
To see the script produced from file1, remove the pipe and the second sed command.
An alternative way would be to use diff and sed:
diff -e file2 file1 | sed 's/d/p/g' | sed -nf - file2

Related

sed & regex expression

I'm trying to add a 'chr' string in the lines where is not there. This operation is necessary only in the lines that have not '##'.
At first I use grep + sed commands, as following, but I want to run the command overwriting the original file.
grep -v "^#" 5b110660bf55f80059c0ef52.vcf | grep -v 'chr' | sed 's/^/chr/g'
So, to run the command in file I write this:
sed -i -E '/^#.*$|^chr.*$/ s/^/chr/' 5b110660bf55f80059c0ef52.vcf
This is the content of the vcf file.
##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="#ref plus strand,#ref minus strand, #alt plus strand, #alt minus strand">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 24430-0009S21_GM17-12140
1 955597 95692 G T 1382 PASS VARTYPE=1;BGN=0.00134309;ARL=150;DER=53;DEA=55;QR=40;QA=39;PBP=1091;PBM=300;TYPE=SNP;DBXREF=dbSNP:rs115173026,g1000:0.2825,esp5400:0.2755,ExAC:0.2290,clinvar:rs115173026,CLNSIG:2,CLNREVSTAT:mult,CLNSIGLAB:Benign;SGVEP=AGRN|+|NM_198576|1|c.45G>T|p.:(p.Pro15Pro)|synonymous GT:DP:AD:DP4 0/1:125:64,61:50,14,48,13
chr1 957898 82729935 G T 1214 off_target VARTYPE=1;BGN=0.00113362;ARL=149;DER=50;DEA=55;QR=38;QA=40;PBP=245;PBM=978;NVF=0.53;TYPE=SNP;DBXREF=dbSNP:rs2799064,g1000:0.3285;SGVEP=AGRN|+|NM_198576|2|c.463+56G>T|.|intronic GT:DP:AD:DP4 0/1:98:47,51:9,38,10,41
If I understand what is your expected result, try:
sed -ri '/^(#|chr)/! s/^/chr/' file
Your question isn't clear and you didn't provide the expected output so we can't test a potential solution but if all you want is to add chr to the start of lines where it's not already present and which don't start with # then that's just:
awk '!/^(#|chr)/{$0="chr" $0} 1' file
To overwrite the original file using GNU awk would be:
awk -i inplace '!/^(#|chr)/{$0="chr" $0} 1' file
and with any awk:
awk '!/^(#|chr)/{$0="chr" $0} 1' file > tmp && mv tmp file
This can be done with a single sed invocation. The script itself is something like the following.
If you have an input of format
$ echo -e '#\n#\n123chr456\n789chr123\nabc'
#
#
123chr456
789chr123
abc
then to prepend chr to non-commented chrless lines is done as
$ echo -e '#\n#\n123chr456\n789chr123\nabc' | sed '/^#/ {p
d
}
/chr/ {p
d
}
s/^/chr/'
which prints
#
#
123chr456
789chr123
chrabc
(Note the multiline sed script.)
Now you only need to run this script on a file in-place (-i in modern sed versions.)

Sed replace pattern with file contents

I would like to use sed (I think?) to replace a pattern with file contents.
Example
File 1 (primary file)
Hello <<CODE>>
Goodbye.
File 2 (contents)
Anonymous person,
I am very nice.
File 3 (target)
Hello Anonymous person,
I am very nice.
Goodbye.
Right now, I am using this command:
sed "/<<CODE>>/{r file2
:a;n;ba}" file1 | \
sed "s/<<CODE>>//g" > \
file3
But this outputs:
Hello
Anonymous person,
I am very nice.
Goodbye.
(note the newline after Hello)
How can I do this without getting that newline?
(note that file2 may contain all sorts of things: brackets, newlines, quotes, ...)
Much simpler to use awk:
awk 'FNR==NR{s=(!s)?$0:s RS $0;next} /<<CODE>>/{sub(/<<CODE>>/, s)} 1' file2 file1
Hello Anonymous person,
I am very nice.
Goodbye.
Explanation:
FNR==NR - Execute this block for first file in input i.e. file2
s=(!s)?$0:s RS $0 - Concatenate whole file content in string s
next - Read next line until EOF on first file
/<<CODE>>/ - If a line with <<CODE>> is found execute that block
sub(/<<CODE>>/, s) - Replace <<CODE>> with string s (data of file2)
1 - print the output
EDIT: Non-regex way:
awk 'FNR==NR{s=(!s)?$0:s RS $0; next}
i=index($0, "<<CODE>>"){$0=substr($0, 1, i-1) s substr($0, i+8)} 1' file2 file1
The awk though it might be harder to read, is probably the right way to go.
Just for comparison sake, here's a ruby version
ruby -ne 'BEGIN{#body=File.open("file2").read}; puts gsub(/<<CODE>>/,#body);' < file1
not too bad in Perl:
cat file1 | perl -e "open FH, qq(file2); \$f2=join '', <FH>; chomp \$f2; map {s/<<CODE>>/\$f2/g; print \$_} <STDIN>" > file3
(maybe i am not the best perl coder)
it's straight-forward. read the whole file2 in, substitute it, then print.
You could do simply with:
awk '{gsub("<<CODE>>", filetwo)}1' filetwo="$(<file2)" file1
I am thinking about a solution where we use Bash to evaluate a cat process outside of the single quotes delimitating the sed script, but unfortunately the following doesn't work as soon as your file2 contains a newline:
sed 's/<<CODE>>/'"$(cat file2)"'/' file1
It accepts spaces in file2, but not newlines, as you can see in the following piece of code that works well, whatever the content of file2:
sed 's/<<CODE>>/'"$(cat file2 | tr -d '\n')"'/' file1
But, obviously, this modifies the content of the file before inclusion, which is simply bad. :-(
So if you want to play, you can first tr the newlines to some weird unexpectable character, and translate those back after sed has worked on its script:
sed 's/<<CODE>>/'"$(cat file2 | tr '\n' '\3')"'/' file1 | tr '\3' '\n'

Using sed to find and replace within matched substrings

I'd like to use sed to process a property file such as:
java.home=/usr/bin/java
groovy-home=/usr/lib/groovy
workspace.home=/build/me/my-workspace
I'd like to replace the .'s and -'s with _'s but only up to the ='s token. The output would be
java_home=/usr/bin/java
groovy_home=/usr/lib/groovy
workspace_home=/build/me/my-workspace
I've tried various approaches including using addresses but I keep failing. Does anybody know how to do this?
What about...
$ echo foo.bar=/bla/bla-bla | sed -e 's/\([^-.]*\)[-.]\([^-.]*=.*\)/\1_\2/'
foo_bar=/bla/bla-bla
This won't work for the case where you have more than 1 dot or dash one the left, though. I'll have to think about it further.
awk makes life easier in this case:
awk -F= -vOFS="=" '{gsub(/[.-]/,"_",$1)}1' file
here you go:
kent$ echo "java.home=/usr/bin/java
groovy-home=/usr/lib/groovy
workspace.home=/build/me/my-workspace"|awk -F= -vOFS="=" '{gsub(/[.-]/,"_",$1)}1'
java_home=/usr/bin/java
groovy_home=/usr/lib/groovy
workspace_home=/build/me/my-workspace
if you really want to do with sed (gnu sed)
sed -r 's/([^=]*)(.*)/echo -n \1 \|sed -r "s:[-.]:_:g"; echo -n \2/ge' file
same example:
kent$ echo "java.home=/usr/bin/java
groovy-home=/usr/lib/groovy
workspace.home=/build/me/my-workspace"|sed -r 's/([^=]*)(.*)/echo -n \1 \|sed -r "s:[-.]:_:g"; echo -n \2/ge'
java_home=/usr/bin/java
groovy_home=/usr/lib/groovy
workspace_home=/build/me/my-workspace
In this case I would use AWK instead of sed:
awk -F"=" '{gsub("\\.|-","_",$1); print $1"="$2;}' <file.properties>
Output:
java_home/usr/bin/java
groovy_home/usr/lib/groovy
workspace_home/build/me/my-workspace
This might work for you (GNU sed):
sed -r 's/=/\n&/;h;y/-./__/;G;s/\n.*\n//' file
"You wait ages for a bus..."
This works with any number of dots and hyphens in the line and does not require GNU sed:
sed 'h; s/.*=//; x; s/=.*//; s/[.-]/_/g; G; s/\n/=/' < data
Here's how:
h: save a copy of the line in the hold space
s: throw away everything before the equal sign in the pattern space
x: swap the pattern and hold
s: blow away everything after the = in the pattern
s: replaces dots and hyphens with underscores
G: join the pattern and hold with a newline
s: replace that newline with an equal to glue it all back together
Other way using sed
sed -re 's/(.*)([.-])(.*)=(.*)/\1_\3=\4/g' temp.txt
Output
java_home=/usr/bin/java
groovy_home=/usr/lib/groovy
workspace_home=/build/me/my-workspace
In case there are more than .- on left hand side then this
sed -re ':a; s/^([^.-]+)([\.-])(.*)=/\1_\3=/1;t a' temp.txt

Regular expression to replace a word with another word on the same line unix

Let A,B,C,D are the words
Input File :
..
A/B/C/D
W/B/C/Z
L/B/C/O
..
Output file:
..
A/B/C/A
W/B/C/W
L/B/C/L
..
Replace the word D with word A one the same line, only if /B/C/ delimiter present in the line and like wise for the other lines
Any sed/awk/perl oneliner to accomplish that
This is a awk solution:
awk -F/ -v OFS=/ '$2=="B" && $3=="C" {$4=$1}1' input.txt
You can do:
sed -re 's/^([^/]*)(\/B\/C\/)([^/]*)$/\1\2\1/' file
Demo:
$ cat file
A/B/C/D
W/B/C/Z
L/B/C/O
$ sed -re 's/^([^/]*)(\/B\/C\/)([^/]*)$/\1\2\1/' file
A/B/C/A
W/B/C/W
L/B/C/L
pearl.306> echo "A/B/C/D"|awk '{split($0,a,"/");print a[1]"/"a[2]"/"a[3]"/"a[1]}'
A/B/C/A
pearl.307>
another way is:
pearl.309> echo "A/B/C/D" | awk -F"/" '{OFS="/"}{$NF=$1;print}'
A/B/C/A
pearl.310>
pearl.318> cat file1
A/B/C/D
W/B/C/Z
L/B/C/O
pearl.319> awk -F"/" '{OFS="/"}{$NF=$1;print}' file1
A/B/C/A
W/B/C/W
L/B/C/L
pearl.320>
This might work for you:
sed 's|^\(\(.\)/B/C/\).|\1\2|' file
if A/B/C/D are real words e.g. wordA/wordB/wordC/wordD, then:
sed 's/|^\(\([^/]*\)/wordB/wordC/\).*|\1\2|' file
This should do the trick. perl -p -e 's/D/A/g'
In sed sed -e 's/D/A/'
perl -pe 's#(/B/C/)(.*)#$1$`#' file
this should work +

Perl, sed, or awk one-liner to change the format of the file

I need advice on how to change the file formatted following way
file1:
A 504688
B jobnameA
A 504690
B jobnameB
A 504691
B jobnameC
...
into file2:
A B
504688 jobnameA
504690 jobnameB
504691 jobnameC
...
One solution I could think of is:
cat file1 | perl -0777 -p -e 's/\s+B/\t/' | awk '{print $2"\t"$3}'.
But I am wondering if there is more efficient way or already known practice that does this job.
perl -nawe 'print "#F[1 .. $#F]", $F[0] eq "A" ? "\t" : "\n"' < /tmp/ab
Look up the options in perlrun.
Another useful one to add is -l (append newline to print), but not in this case.
Assuming your input file is tab separated:
echo $'A\tB'
cut -f2 filename | paste - -
Should be pretty quick because this is exactly what cut and paste were written to do.
awk '/^A/{num=$2}/^B/{print num,$2}' file
Or, alternately,
awk '{num=$2;getline;print num,$2}' file
Here is an sed solution:
sed -e 'N' -e 's/A\s*\(.*\)\nB\s*\(.*\)/\1\t\2/' file
This version will also print the header at the top:
sed '1{h;s/.*/A\tB/p;g};N;s/A\s*\(.*\)\nB\s*\(.*\)/\1\t\2/' file
Or an alternative:
sed -n '/^A\s*/{s///;h};/^B\s*/{s///;H;g;s/\n/\t/p}' file
If your sed does not support semicolons as a command separator for the alternative:
sed -n '
/^A\s*/{ # if the line starts with "A"
s/// # remove the "A" and the whitespace
h # copy the remainder into the hold space
} # end if
/^B\s*/{ # if the line starts with "B"
s/// # remove the "B" and the whitespace
H # append pattern space to hold space
g # copy hold space to pattern space
s/\n/\t/p # replace newline with tab and print
}' file
This version will also print the header at the top:
sed -n '/^A\s*/{s///;h;1s/.*/A\tB/p};/^B\s*/{s///;H;g;s/\n/\t/p}' file
This will work with any header text, not just fixed A and B >>
awk '{a=$1;b=$2;getline;if(c!=1){print a,$1;c=1};print b,$2}' file1 >file2
...and it will print also header row
If you need \t separator, then use:
awk '{a=$1;b=$2;getline;if(c!=1){print a"\t"$1;c=1};print b"\t"$2}' file1 >file2
This might work for you:
sed -e '1i\A\tB' -e 'N;s/A\s*\(\S*\).*\nB\s*\(\S*\).*/\1\t\2/' file