I need to find two numbers from lines which look like this
>Chr14:453901-458800
I have a large quantity of those lines mixed with lines that doesn't contain ":" so we can search for colon to find the line with numbers. Every line have different numbers.
I need to find both numbers after ":" which are separated by "-" then substract the first number from the second one and print result on the screen for each line
I'd like this to be done using awk
I managed to do something like this:
awk -e '$1 ~ /\:/ {print $0}' file.txt
but it's nowhere near the end result
For this example i showed above my result would be:
4899
Because it is the result of 458800 - 453901 = 4899
I can't figure it out on my own and would appreciate some help
With GNU awk. Separate the row into multiple columns using the : and - separators. In each row containing :, subtract the contents of column 2 from the contents of column 3 and print result.
awk -F '[:-]' '/:/{print $3-$2}' file
Output:
4899
Using awk
$ awk -F: '/:/ {split($2,a,"-"); print a[2] - a[1]}' input_file
4899
I have a .txt file like this:
ENST00000000442 64073050 64074640 64073208 64074651 ESRRA
ENST00000000233 127228399 127228552 ARF5
ENST00000003100 91763679 91763844 CYP51A1
I want to get only the last 3 columns of each line.
as you see some times there are some empty lines between 2 lines which must be ignored. here is the output that I want to make:
64073208 64074651 ESRRA
127228399 127228552 ARF5
91763679 91763844 CYP51A1
awk '/a/ {print $1- "\t" $-2 "\t" $-3}' file.txt.
it does not return what I want. do you know how to correct the command?
Following awk may help you in same.
awk 'NF{print $(NF-2),$(NF-1),$NF}' OFS="\t" Input_file
Output will be as follows.
64073208 64074651 ESRRA
127228399 127228552 ARF5
91763679 91763844 CYP51A1
EDIT: Adding explanation of command too now.(NOTE this following command is for only explanation purposes one should run above command only to get the results)
awk 'NF ###Checking here condition NF(where NF is a out of the box variable for awk which tells number of fields in a line of a Input_file which is being read).
###So checking here if a line is NOT NULL or having number of fields value, if yes then do following.
{
print $(NF-2),$(NF-1),$NF###Printing values of $(NF-2) which means 3rd last field from current line then $(NF-1) 2nd last field from line and $NF means last field of current line.
}
' OFS="\t" Input_file ###Setting OFS(output field separator) as TAB here and mentioning the Input_file here.
You can use sed too
sed -E '/^$/d;s/.*\t(([^\t]*[\t|$]){2})/\1/' infile
With some piping:
$ cat file | tr -s '\n' | rev | cut -f 1-3 | rev
64073208 64074651 ESRRA
127228399 127228552 ARF5
91763679 91763844 CYP51A1
First, cat the file to tr to squeeze out repeted \ns to get rid of empty lines. Then reverse the lines, cut the first three fields and reverse again. You could replace the useless cat with the first rev.
I need to know if I can match awk value while I am inside a piped command. Like below:
somebinaryGivingOutputToSTDOUT | grep -A3 "sometext" | grep "somemoretext" | awk -F '[:|]' 'BEGIN{OFS=","; print "Col1,Col2,Col3,Col4"}{print $4,$6,$4*10^10+$6,$8}'
from here I need to check if the computed value $4*10^10+$6 is present (matches to) in any of the column value of another file. If it is present then print, else just move forward.
File where value needs to be matched is as below:
a,b,c,d,e
1,2,30000000000,3,4
I need to match with the 3rd column of the above file.
I would ideally like this to be in the same command, because if this check is not applied, it prints more than 100 million rows (and a large file).
I have already read this question.
Adding more info:
Breaking my command into parts
part1-command:
somebinaryGivingOutputToSTDOUT | grep -A3 "sometext" | grep "Something:"
part1-output(just showing 1 iteration output):
Something:38|Something1:1|Something2:10588429|Something3:1491539456372358463
part2-command Now I use awk
awk -F '[:|]' 'BEGIN{OFS=","; print "Col1,Col2,Col3,Col4"}{print $4,$6,$4*10^10+$6,$8}'
part2-command output: currently below values are printed (see how i multiplied 1*10^10+10588429 and got 10010588429
1,10588429,10010588429,1491539456372358463
3,12394810,30012394810,1491539456372359082
1,10588430,10010588430,1491539456372366413
Now here I need to put a check (within the command [near awk]) to print only if 10010588429 was present in another file (say another_file.csv as below)
another_file.csv
A,B,C,D,E
1,2, 10010588429,4,5
x,y,z,z,k
10,20, 10010588430,40,50
output should only be
1,10588429,10010588429,1491539456372358463
1,10588430,10010588430,1491539456372366413
So for every row of awk we check entry in file2 column C
Using the associative array approach in previous question, include a hyphen in place of the first file to direct AWK to the input stream.
Example:
grep -A3 "sometext" | grep "somemoretext" | awk -F '[:|]'
'BEGIN{OFS=","; print "Col1,Col2,Col3,Col4"}
NR==FNR {
query[$4*10^10+$6]=$4*10^10+$6;
out[$4*10^10+$6]=$4 FS $6 FS $4*10^10+$6 FS $8;
next
}
query[$3]==$3 {
print out[$3]
}' - another_file.csv > output.csv
More info on the merging process in the answer cited in the question:
Using AWK to Process Input from Multiple Files
I'll post a template which you can utilize for your computation
awk 'BEGIN {FS=OFS=","}
NR==FNR {lookup[$3]; next}
/sometext/ {c=4}
c&&c--&&/somemoretext/ {value= # implement your computation here
if(value in lookup)
print "what you want"}' lookup.file FS=':' grep.files...
here awk loads up the values in the third column of the first file (which is comma delimited) into the lookup array (a hashmap in disguise). For the next set of files, sets the delimiter to : and similar to grep -A3 looks within the 3 distance of the first pattern for the second pattern, does the computation and prints what you want.
In awk you can have more control on what column your pattern matches as well, here I replicated grep example.
This is another simplified example to focus on the core of the problem.
awk 'BEGIN{for(i=1;i<=1000;i++) print int(rand()*1000), rand()}' |
awk 'NR==FNR{lookup[$1]; next}
$1 in lookup' perfect.numbers -
first process creates 1000 random records, and second one filters the ones where the first fields is in the look up table.
28 0.736027
496 0.968379
496 0.404218
496 0.151907
28 0.0421234
28 0.731929
for the lookup file
$ head perfect.numbers
6
28
496
8128
the piped data is substituted as the second file at -.
You can pipe your grep or awk output into a while read loop which gives you some degree of freedom. There you could decide on whether to forward a line:
grep -A3 "sometext" | grep "somemoretext" | while read LINE; do
COMPUTED=$(echo $LINE | awk -F '[:|]' 'BEGIN{OFS=","}{print $4,$6,$4*10^10+$6,$8}')
if grep $COMPUTED /the/file/to/search &>/dev/null; then
echo $LINE
fi
done | cat -
I have a requirement to print the first string of a line if last 5 strings match specific input.
Example: Specified input is 2
India;1;2;3;4;5;6
Japan;1;2;2;2;2;2
China;2;2;2;2
England;2;2;2;2;2
Expected Output:
Japan
England
As you can see, China is excluded as it doesn't meet the requirement (last 5 digits have to be matched with the input).
grep ';2;2;2;2;2$' file | cut -d';' -f1
$ in a regex stands for "end of line", so grep will print all the lines that end in the given string
-d';' tells cut to delimit columns by semicolons
-f1 outputs the first column
You could use awk:
awk -F';' -v v="2" -v count=5 '
{
c=0;
for(i=2;i<=NF;i++){
if($i == v) c++
if(c>=count){print $1;next}
}
}' file
where
v is the value to match
count is the maximum number of value to print the wanted string
the for loop is parsing all fields delimited with a ; in order to find a match
This script doesn't need the 5 values 2 to be consecutive.
With sed:
sed -n 's/^\([^;]*\).*;2;2;2;2;2$/\1/p' file
It captures and output non ; first characters in lines ending with ;2;2;2;2;2
It can be shortened with GNU sed to:
sed -nE 's/^([^;]*).*(;2){5}$/\1/p' file
awk -F\; '/;2;2;2;2;2$/{print $1}' file
Japan
England
I have a tab separated file with 3 columns. I'd like to get the contents of the first column, but only for the rows where the 3rd column is equal to 8. How do I extract these values? If I just wanted to extract the values in the first column, I would do the following:
cat file1 | tr "\t" "~" | cut -d"~" -f1 >> file_with_column_3
I'm thinking something like:
cat file1 | tr "\t" "~" | if cut -d"~" -f3==8; then cut -d"~" -f1 ; fi>> file_with_column_3
But that doesn't quite seem to work.
Given that your file is tab delimited, it seems like this problem would be well suited for awk.
Something simple like below should work for you, though without any sample data I can't say for sure (try to always include this on questions on SO)
awk -F'\t' '$3==8 {print $1}' inputfile > outputfile
The -F'\t' sets the input delimiter as tab.
$3==8 compares if the 3rd column based on that delimiter is 8.
If so, the {print $1} is executed, which prints the first column.
Otherwise, nothing is done and awk proceeds to the next line.
If your file had a header you wanted to preserve, you could just modify this like the following, which tells awk to print if the current record number is 1.
awk -F'\t' 'NR==1 {print;} $3==8 {print $1}' inputfile > outputfile
awk can handle this better:
awk -F '\t' '$3 == 8 { print $1 }' file1
You can do it with bash only too:
cat x | while read y; do split=(${y}); [ ${split[2]} == '8' ] && echo $split[0]; done
The input is read in variable y, then split into an array. The IFS (input field separator) defaults to <space><tab<>newline>, so it splits on tabs too. The third field of the array is then compared to '8'. If it equals, it prints the first field of the array. Remember that fields in arrays start counting at zero.