I am trying out one script in which a file [ file.txt ] has so many columns like
abc|pqr|lmn|123
pqr|xzy|321|azy
lee|cha| |325
xyz| |abc|123
I would like to get the column list in bash script using awk command if column is empty it should print blank else print the column value
I have tried the below possibilities but it is not working
cat file.txt | awk -F "|" {'print $2'} | sed -e 's/^$/blank/' // Using awk and sed
cat file.txt | awk -F "|" '!$2 {print "blank"} '
cat file.txt | awk -F "|" '{if ($2 =="" ) print "blank" } '
please let me know how can we do that using awk or any other bash tools.
Thanks
I think what you're looking for is
awk -F '|' '{print match($2, /[^ ]/) ? $2 : "blank"}' file.txt
match(str, regex) returns the position in str of the first match of regex, or 0 if there is no match. So in this case, it will return a non-zero value if there is some non-blank character in field 2. Note that in awk, the index of the first character in a string is 1, not 0.
Here, I'm assuming that you're interested only in a single column.
If you wanted to be able to specify the replacement string from a bash variable, the best solution would be to pass the bash variable into the awk program using the -v switch:
awk -F '|' -v blank="$replacement" \
'{print match($2, /[^ ]/) ? $2 : blank}' file.txt
This mechanism avoids problems with escaping metacharacters.
You can do it using this sed script:
sed -r 's/\| +\|/\|blank\|/g' File
abc|pqr|lmn|123
pqr|xzy|321|azy
lee|cha|blank|325
xyz|blank|abc|123
If you don't want the |:
sed -r 's/\| +\|/\|blank\|/g; s/\|/ /g' File
abc pqr lmn 123
pqr xzy 321 azy
lee cha blank 325
xyz blank abc 123
Else with awk:
awk '{gsub(/\| +\|/,"|blank|")}1' File
abc|pqr|lmn|123
pqr|xzy|321|azy
lee|cha|blank|325
xyz|blank|abc|123
You can use awk like this:
awk 'BEGIN{FS=OFS="|"} {for (i=1; i<=NF; i++) if ($i ~ /^ *$/) $i="blank"} 1' file
abc|pqr|lmn|123
pqr|xzy|321|azy
lee|cha|blank|325
xyz|blank|abc|123
Related
I have a csv file with dynamic columns.
I've tried to use awk -F , 'NF>1' resul1.txt but it still prints all columns.
Since it has dynamic columns.
Its quite difficult to print using print $1 till end.
Try this awk command:
awk -F, '{$1=""}1' input.txt | awk -vOFS=, '{$1=$1}1' > output.txt
Make the 1st field empty
Print out entire line again
try substr function :
substr(string, start [, length ])
Return a length-character-long substring of string, starting at character number start. The first character of a string is character
number one.For example, substr("washington", 5, 3) returns "ing".*
awk -F, '{print substr($0,length($1)+1+length(FS))}' file
You can use cut:
cut -d',' -f2- yourfile.csv > output.csv
Explanation:
-d - setting delimiter to ,
-f - fields to print
2- - from 2 field to end of line
With awk:
awk -F, '{sub(/[^,]+,/,"",$0);}1' OFS=, yourfile.csv > output.csv
With sed:
sed -i.bak 's/^[^,]\+,//g' yourfile.csv
-i - in-place edit
I'm trying to figure out how to make a .txt file (myGeneFile.txt) of IDs and genes that looks like this:
Probe Set ID Gene Symbol
1007_s_at DDR1 /// MIR4640
1053_at RFC2
117_at HSPA6
121_at PAX8
1255_g_at GUCA1A
1294_at MIR5193 /// UBA7
into this:
DDR1
MIR4640
RFC2
HSPA6
PAX8
GUCA1A
MIR5193
UBA
First I tried doing this:
cat myGeneFile.txt | tail -n +2 | awk '{split($2,a,"///"); print a[1] "\t" a[2] "\t" a[3] "\t" a[4] "\t" a[5];}' > test.txt
(i.e., I removed the top (header) line of the file, I tried splitting the second line along the delimiter ///, and then printing any genes that might appear)
Then, I tried doing this:
cat myGeneFile.txt | tail -n +2 | awk '{print $2}' | grep -o -E '\w+' > test.txt
(literally listing out all of the words in the second column)
I got the same output in both cases - a long list of just the first gene in each row (e.g. so MIR4640 and UBA7 were mising)
Any ideas?
EDIT: Thanks #CodeGnome for your help. I ended up using that code and modifying it because I discovered that my file had between 1 and 30 different gene names on each row. So, I used:
awk 'NR == 1 {next}
{
sub("///", "")
print $2 }
{ for (i=3; i<=30; i++)
if ($i) {print $i}
}' myGeneFile.txt > test2.txt
#GlenJackson also had a solution that worked really well:
awk 'NR>1 {for (i=2; i<=NF; i++) if ($i != "///") print $i}' file
My awk take:
awk 'NR>1 {for (i=2; i<=NF; i++) if ($i != "///") print $i}' file
or sed
sed '
1d # delete the header
s/[[:blank:]]\+/ /g # squeeze whitespace
s/^[^ ]\+ // # remove the 1st word
s| ///||g # delete all "///" words
s/ /\n/g # replace spaces with newlines
' file
Use Conditional Print Statements Inside an AWK Action
The following gives the desired output by removing unwanted characters with sub(), and then using multiple print statements to create the line breaks. The second print statement is conditional, and only triggers when the third field isn't empty; this avoids creating extraneous empty lines in the output.
$ awk 'NR == 1 {next}
{
sub("///", "")
print $2
if ($3) {print $3}
}' myGeneFile.txt
DDR1
MIR4640
RFC2
HSPA6
PAX8
GUCA1A
MIR5193
UBA7
This will work:
tail -n+2 tmp | sed -E 's/ +/ /' | cut -d' ' -f2- | sed 's_ */// *_\n_'
Here's what is happening:
tail -n+2 Strip off the header
sed -E 's/ +/ /' Condense the whitespace
cut -d' ' -f2- Use cut to select all fields but the first, using a single space as the delimiter
sed 's_ */// *_\n_' Convert all /// (and any surrounding whitespace) to a newline
You don't need the initial cat, it's usually better to simply pass the input file as an argument to the first command. If you want the file name in a place that is easy to change, this is a better option as it avoids the additional process (and I find it easier to change the file if it's at the end):
(tail -n+2 | sed -E 's/ +/ /' | cut -d' ' -f2- | sed 's_ */// *_\n_') < tmp
Given the existing input and the modified requirement (from the comment on Morgen's answer) the following should do what you want (for any number of gene columns).
awk 'NR > 1 {
p=0
for (i = 2; i <= NF; i++) {
if ($i == "///") {
p=1
continue
}
printf "%s%s\n", p?"n":"", $i
}
}' input.txt
Your criteria for selecting which strings to output is not entirely clear, but here's another command that at least produces your expected output:
tail -n +2 myGeneFile.txt | grep -oE '\<[A-Z][A-Z0-9]*\>'
It basically just 1) skips the first line and 2) finds all other words (delimited by non-word characters and/or start/end of line) that consist entirely of uppercase letters or digits, with the first being a letter.
Here is my code that I want to use to separate 3 columns from hist.txt into 2 separate files, hist1.dat with first and second column and hist2.dat with first and third column. The columns in hist.txt may be separated with more than one space. I want to save in histogram1.dat and histogram2.dat the first n lines until the last nonzero value.
The script creates histogram1.dat correct, but histogram2.dat contains all the lines from hist2.dat.
hist.txt is like :
http://pastebin.com/JqgSKZrP
#!bin/bash
sed 's/\t/ /g' hist.txt | awk '{print $1 " " $2;}' > hist1.dat
sed 's/\t/ /g' hist.txt | awk '{print $1 " " $3;}' > hist2.dat
head -n $( awk 'BEGIN {last=1}; {if($2!=0) last=NR};END {print last}' hist1.dat) hist1.dat > histogram1.dat
head -n $( awk 'BEGIN {last=1}; {if($2!=0) last=NR};END {print last}' hist2.dat) hist2.dat > histogram2.dat
What is the cause of this problem? Might it be due to some special restriction with head?
Thanks.
For your first histogram, try
awk '$2 ~ /000000/{exit}{print $1, $2}' hist.txt
and for your second:
awk '$3 ~ /000000/{exit}{print $1, $3}' hist.txt
Hope I understood you correctly...
I have a line like:
one:two:three:four:five:six seven:eight
and I want to use awk to get $1 to be one and $2 to be two:three:four:five:six seven:eight
I know I can get it by doing sed before. That is to change the first occurrence of : with sed then awk it using the new delimiter.
However replacing the delimiter with a new one would not help me since I can not guarantee that the new delimiter will not already be somewhere in the text.
I want to know if there is an option to get awk to behave this way
So something like:
awk -F: '{print $1,$2}'
will print:
one two:three:four:five:six seven:eight
I will also want to do some manipulations on $1 and $2 so I don't want just to substitute the first occurrence of :.
Without any substitutions
echo "one:two:three:four:five" | awk -F: '{ st = index($0,":");print $1 " " substr($0,st+1)}'
The index command finds the first occurance of the ":" in the whole string, so in this case the variable st would be set to 4. I then use substr function to grab all the rest of the string from starting from position st+1, if no end number supplied it'll go to the end of the string. The output being
one two:three:four:five
If you want to do further processing you could always set the string to a variable for further processing.
rem = substr($0,st+1)
Note this was tested on Solaris AWK but I can't see any reason why this shouldn't work on other flavours.
Some like this?
echo "one:two:three:four:five:six" | awk '{sub(/:/," ")}1'
one two:three:four:five:six
This replaces the first : to space.
You can then later get it into $1, $2
echo "one:two:three:four:five:six" | awk '{sub(/:/," ")}1' | awk '{print $1,$2}'
one two:three:four:five:six
Or in same awk, so even with substitution, you get $1 and $2 the way you like
echo "one:two:three:four:five:six" | awk '{sub(/:/," ");$1=$1;print $1,$2}'
one two:three:four:five:six
EDIT:
Using a different separator you can get first one as filed $1 and rest in $2 like this:
echo "one:two:three:four:five:six seven:eight" | awk -F\| '{sub(/:/,"|");$1=$1;print "$1="$1 "\n$2="$2}'
$1=one
$2=two:three:four:five:six seven:eight
Unique separator
echo "one:two:three:four:five:six seven:eight" | awk -F"#;#." '{sub(/:/,"#;#.");$1=$1;print "$1="$1 "\n$2="$2}'
$1=one
$2=two:three:four:five:six seven:eight
The closest you can get with is with GNU awk's FPAT:
$ awk '{print $1}' FPAT='(^[^:]+)|(:.*)' file
one
$ awk '{print $2}' FPAT='(^[^:]+)|(:.*)' file
:two:three:four:five:six seven:eight
But $2 will include the leading delimiter but you could use substr to fix that:
$ awk '{print substr($2,2)}' FPAT='(^[^:]+)|(:.*)' file
two:three:four:five:six seven:eight
So putting it all together:
$ awk '{print $1, substr($2,2)}' FPAT='(^[^:]+)|(:.*)' file
one two:three:four:five:six seven:eight
Storing the results of the substr back in $2 will allow further processing on $2 without the leading delimiter:
$ awk '{$2=substr($2,2); print $1,$2}' FPAT='(^[^:]+)|(:.*)' file
one two:three:four:five:six seven:eight
A solution that should work with mawk 1.3.3:
awk '{n=index($0,":");s=$0;$1=substr(s,1,n-1);$2=substr(s,n+1);print $1}' FS='\0'
one
awk '{n=index($0,":");s=$0;$1=substr(s,1,n-1);$2=substr(s,n+1);print $2}' FS='\0'
two:three:four five:six:seven
awk '{n=index($0,":");s=$0;$1=substr(s,1,n-1);$2=substr(s,n+1);print $1,$2}' FS='\0'
one two:three:four five:six:seven
Just throwing this on here as a solution I came up with where I wanted to split the first two columns on : but keep the rest of the line intact.
Comments inline.
echo "a:b:c:d::e" | \
awk '{
split($0,f,":"); # split $0 into array of fields `f`
sub(/^([^:]+:){2}/,"",$0); # remove first two "fields" from `$0`
print f[1],f[2],$0 # print first two elements of `f` and edited `$0`
}'
Returns:
a b c:d::e
In my input I didn't have to worry about the first two fields containing escaped :, if that was a requirement, this solution wouldn't work as expected.
Amended to match the original requirements:
echo "a:b:c:d::e" | \
awk '{
split($0,f,":");
sub(/^([^:]+:)/,"",$0);
print f[1],$0
}'
Returns:
a b:c:d::e
I am working on the following bash script:
# contents of dbfake file
1 100% file 1
2 99% file name 2
3 100% file name 3
#!/bin/bash
# cat out data
cat dbfake |
# select lines containing 100%
grep 100% |
# print the first and third columns
awk '{print $1, $3}' |
# echo out id and file name and log
xargs -rI % sh -c '{ echo %; echo "%" >> "fake.log"; }'
exit 0
This script works ok, but how do I print everything in column $3 and then all columns after?
You can use cut instead of awk in this case:
cut -f1,3- -d ' '
awk '{ $2 = ""; print }' # remove col 2
If you don't mind a little whitespace:
awk '{ $2="" }1'
But UUOC and grep:
< dbfake awk '/100%/ { $2="" }1' | ...
If you'd like to trim that whitespace:
< dbfake awk '/100%/ { $2=""; sub(FS "+", FS) }1' | ...
For fun, here's another way using GNU sed:
< dbfake sed -r '/100%/s/^(\S+)\s+\S+(.*)/\1\2/' | ...
All you need is:
awk 'sub(/.*100% /,"")' dbfake | tee "fake.log"
Others responded in various ways, but I want to point that using xargs to multiplex output is rather bad idea.
Instead, why don't you:
awk '$2=="100%" { sub("100%[[:space:]]*",""); print; print >>"fake.log"}' dbfake
That's all. You don't need grep, you don't need multiple pipes, and definitely you don't need to fork shell for every line you're outputting.
You could do awk ...; print}' | tee fake.log, but there is not much point in forking tee, if awk can handle it as well.