I wanted to do a simple parsing of two files with ids and some corresponding numerical values. I didn't want awk to print numbers in scientific notation.
File looks like this:
someid-1 860025 50.0401 4.00022
someid-2 384319 22.3614 1.78758
someid-3 52096 3.03118 0.242314
someid-4 43770 2.54674 0.203587
someid-5 33747 1.96355 0.156967
someid-6 20281 1.18004 0.0943328
someid-7 12231 0.711655 0.0568899
someid-8 10936 0.636306 0.0508665
someid-9 10224.8 0.594925 0.0475585
someid-10 10188.8 0.59283 0.047391
when use print instead of printf :
awk 'BEGIN{FS=OFS="\t"} NR==FNR{x[$1]=$0;next} ($1 in x){split(x[$1],k,FS); print $1,k[2],k[3],k[4],$2,$3,$4}' OSCAo.txt dme_miRNA_PIWI_OSC.txt | sort -n -r -k 7 | head
i get this result:
dme-miR-iab-4-5p 0.333333 0.000016 0.000001 0.25 0.000605606 9.36543e-07
dme-miR-9c-5p 10987.300000 0.525413 0.048798 160.2 0.388072 0.000600137
dme-miR-9c-3p 731.986000 0.035003 0.003251 2.10714 0.00510439 7.89372e-06
dme-miR-9b-5p 30322.500000 1.450020 0.134670 595.067 1.4415 0.00222922
dme-miR-9b-3p 2628.280000 0.125684 0.011673 48 0.116276 0.000179816
dme-miR-9a-3p 10.365000 0.000496 0.000046 0.25 0.000605606 9.36543e-07
dme-miR-999-5p 103.433000 0.004946 0.000459 0.0769231 0.00018634 2.88167e-07
dme-miR-999-3p 1513.790000 0.072389 0.006723 28 0.0678278 0.000104893
dme-miR-998-5p 514.000000 0.024579 0.002283 73 0.176837 0.000273471
dme-miR-998-3p 3529.000000 0.168756 0.015673 42 0.101742 0.000157339
Notice the scientific notation in the last column
I understand that printf with appropriate format modifier can do the job but the code becomes very lengthy. I have to write something like this:
awk 'BEGIN{FS=OFS="\t"} NR==FNR{x[$1]=$0;next} ($1 in x){split(x[$1],k,FS); printf "%s\t%3.6f\t%3.6f\t%3.6f\t%3.6f\t%3.6f\t%3.6f\n", $1,k[2],k[3],k[4],$2,$3,$4}' file1.txt file2.txt > fileout.txt
This becomes clumsy when I have to parse fileout with another similarly structured file.
Is there any way to specify default numerical output, such that any string will be printed like a string but all numbers follow a particular format.
I think You misinterpreted the meaning of %3.6f. The first number before the decimal point is the field width not the "number of digits before decimal point". (See prinft(3))
So You should use %10.6f instead. It can be tested easily in bash
$ printf "%3.6f\n%3.6f\n%3.6f" 123.456 12.345 1.234
123.456000
12.345000
1.234000
$ printf "%10.6f\n%10.6f\n%10.6f" 123.456 12.345 1.234
123.456000
12.345000
1.234000
You can see that the later aligns to the decimal point properly.
As sidharth c nadhan mentioned You can use the OFMT awk internal variable (seem awk(1)). An example:
$ awk 'BEGIN{print 123.456; print 12.345; print 1.234}'
123.456
12.345
1.234
$ awk -vOFMT=%10.6f 'BEGIN{print 123.456; print 12.345; print 1.234}'
123.456000
12.345000
1.234000
As I see in You example the number with maximum digits can be 123456.1234567, so the format %15.7f to cover all and show a nice looking table.
But unfortunately it will not work if the number has no decimal point in it or even if it does, but it ends with .0.
$ awk -vOFMT=%15.7f 'BEGIN{print 123.456;print 123;print 123.0;print 0.0+123.0}'
123.4560000
123
123
123
I even tried gawk's strtonum() function, but the integers are considered as non-OFMT strings. See
awk -vOFMT=%15.7f -vCONVFMT=%15.7f 'BEGIN{print 123.456; print strtonum(123); print strtonum(123.0)}'
It has the same output as before.
So I think, you have to use printf anyway. The script can be a little bit shorter and a bit more configurable:
awk -vf='\t'%15.7f 'NR==FNR{x[$1]=sprintf("%s"f f f,$1,$2,$3,$4);next}$1 in x{printf("%s"f f f"\n",x[$1],$2,$3,$4)}' file1.txt file2.txt
The script will not work properly if there are duplicated IDs in the first file. If it does not happen then the two conditions can be changed and the ;next can be left off.
awk 'NR==FNR{x[$1]=$0;next} ($1 in x){split(x[$1],k,FS); printf "%s\t%9s\t%9s\t%9s\t%9s\t%9s\t%9s\n", $1,k[2],k[3],k[4],$2,$3,$4}' file1.txt file2.txt > fileout.txt
Related
I have a csv file that contains this kind of values:
vm47,8,32794384Ki,16257320Ki
vm47,8,30223304245,15223080Ki
vm48,8,32794384Ki,16257312Ki
vm48,8,30223304245,15223072Ki
vm49,8,32794384Ki,16257320Ki
vm49,8,30223304245,15223080Ki
The columns 3 and 4 are memoy values expressed either in bytes, or kibibytes. The problem is that the "Ki" string appears randomly through the CSV file, particularly in column3, it's inconsistent.
So to make the file consistent, I need to convert everything in bytes. So basically, any value matching a trailing "Ki" needs to have its numeric value multiplied by 1024, and then replace the corresponding XXXXXKi match.
The reason why I want to do it with awk is because I am already using awk to generate that csv format, but I am happy to do it with sed too.
This is my code so far but obviously it's wrong as it's multiplying any value in columns 3 and 4 by 1024 even though it does not match "Ki". I am not sure at this point how to ask awk "if you see Ki at the end, then multiply by 1024".
kubectl describe node --context=$context| sed -E '/Name:|cpu:|ephemeral-storage:|memory:/!d' | sed 's/\s//g' | awk '
BEGIN {FS = ":"; OFS = ","}
{record[$1] = $2}
$1 == "memory" {print record["Name"], record["cpu"], record["ephemeral-storage"], record["memory"]}
' | awk -F, '{print $1,$2,$3,$3*1024,$4,$4*1024}' >> describe_nodes.csv
Edit: I made a mistake, you need to multiply by 128 to convert KiB in bytes, not 1024.
"if you see Ki at the end, then multiply by 1024
You may use:
awk 'BEGIN{FS=OFS=","} $3 ~ /Ki$/ {$3 *= 1024} $4 ~ /Ki$/ {$4 *= 1024} 1' file
vm47,8,33581449216,16647495680
vm47,8,30223304245,15588433920
vm48,8,33581449216,16647487488
vm48,8,30223304245,15588425728
vm49,8,33581449216,16647495680
vm49,8,30223304245,15588433920
Or a bit shorter:
awk 'BEGIN{FS=OFS=","} {
for (i=3; i<=4; ++i) $i ~ /Ki$/ && $i *= 1024} 1' file
With your shown samples/attempts, please try following awk code. Simple explanation would be, traverse through fields from 3rd field onwards and look for if a value has Ki(ignore cased manner) then multiply it with 128, print all edited/non-edited lines at last.
awk 'BEGIN{FS=OFS=","} {for(i=3;i<=NF;i++){if($i~/[Kk][Ii]$/){$i *= 128}}} 1' Input_file
You could try numfmt:
$ numfmt -d, --field 3,4 --from=auto --to=none <<EOF
vm47,8,32794384Ki,16257320Ki
vm47,8,30223304245,15223080Ki
EOF
vm47,8,33581449216,16647495680
vm47,8,30223304245,15588433920
I am puzzeled by the differences in the following two awk-lines:
$ cat a.txt
1
$ awk '{$2=$1/1982300000 ;$3 = $2 * 0.05}{print $1"\t"$2"\t"$3}' a.txt
1 5.04465e-10 2.52232e-11
$ awk '{$2=$1/1.98*10^09 ;$3 = $2 * 0.05}{print $1"\t"$2"\t"$3}' a.txt
1 5.05051e+08 2.52525e+07
I think I am writing the exponential notation in awk somehow wrong can you please correct
here
$ echo 1 | awk -v OFS='\t' '{print $1, a=$1/(1.98*10^9), a*0.05}'
1 5.05051e-10 2.52525e-11
you need add parenthesis, otherwise the second multiplication (10^9) is not in the denominator.
Or, you can use the e notation
$ echo 1 | awk -v OFS='\t' '{print $1, a=$1/1.98e9, a*0.05}'
which doesn't require extra parans.
There are a couple of things here you have to take into account:
Numbers that are written in scientific notation of the form 1.23 × 10-4 are best written in E-notation when it boils down to programming. The most common form of E-notation is 1.23E4 or 1.23e4.
When you would write 1.23*10^4 (under the assumption that ^ represents Exponentiation), you will actively perform an exponentiation operation to compute how much 10^4 is, followed by a multiplication of two numbers. This looks very expensive to define a single number.
Multiplication is not associative with a division. This means that a/b*c is different from a/(b*c).
Hence, the solution to your problem is thus:
Use E-notation:
awk '{$2=$1/1.98e9 ;$3 = $2 * 0.05}{print $1"\t"$2"\t"$3}' a.txt
Or add brackets:
awk '{$2=$1/(1.98*10^9) ;$3 = $2 * 0.05}{print $1"\t"$2"\t"$3}' a.txt
this is my data - i've more than 1000rows . how to get only the the rec's with numbers in it.
Records | Num
123 | 7 Y1 91
7834 | 7PQ34-102
AB12AC|87 BWE 67
5690278| 80505312
7ER| 998
Output has to be
7ER| 998
5690278| 80505312
I'm new to linux programming, any help would be highly useful to me. thanks all
I would use awk:
awk -F'[[:space:]]*[|][[:space:]]*' '$2 ~ /^[[:digit:]]+$/'
If you want to print the number of lines deleted as you've been asking in comments, you may use this:
awk -F'[[:space:]]*[|][[:space:]]*' '
{
if($2~/^[[:digit:]]+$/){print}else{c++}
}
END{printf "%d lines deleted\n", c}' file
A short and simple GNU awk (gawk) script to filter lines with numbers in the second column (field), assuming a one-word field (e.g. 1234, or 12AB):
awk -F'|' '$2 ~ /\y[0-9]+\y/' file
We use the GNU extension for regexp operators, i.e. \y for matching the word boundary. Other than that, pretty straightforward: we split fields on | and look for isolated digits in the second field.
Edit: Since the question has been updated, and now explicitly allows for multiple words in the second field (e.g. 12 AB, 12-34, 12 34), to get lines with numbers and separators only in the second field:
awk -F'|' '$2 ~ /^[- 0-9]+$/' file
Alternatively, if we say only letters are forbidden in the second field, we can use:
awk -F'|' '$2 ~ /^[^a-zA-Z]+$/' file
I have multiple files that look like the one below. They are tab-separated. For all the files I would like to take out column 1 and the column that start with XF:Z:. This will give me output 1
The files names are htseqoutput*.sam.sam where * varies. I am not sure about the awk function use, and if the for-loop is correct.
for f in htseqoutput*.sam.sam
do
awk ????? "$f" > “out${f#htseqoutput}”
done
input example
AACAGATGATGAACTTATTGACGGGCGGACAGGAACTGTGTGCTGATTGTC_11 16 chr22 39715068 24 51M * 0 0 GACAATCAGCACACAGTTCCTGTCCGCCCGTCAATAAGTTCATCATCTGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:18T31G0 YT:Z:UU XF:Z:SNORD43
GTTTCCTTAGTGTAGCGGTTATCACATTCGCCT_0 16 chr19 4724687 40 33M * 0 0 AGGCGAATGTGATAACCGCTACACTAAGGAAAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:26C6 YT:Z:UU XF:Z:tRNA
TCGACTCCCGGTGTGGGAACC_0 16 chr13 45492060 23 21M * 0 0 GGTTCCCACACCGGGAGTCGA IIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:0C20 YT:Z:UU XF:Z:tRNA
output 1:
AACAGATGATGAACTTATTGACGGGCGGACAGGAACTGTGTGCTGATTGTC_11 SNORD43
GTTTCCTTAGTGTAGCGGTTATCACATTCGCCT_0 tRNA
TCGACTCCCGGTGTGGGAACC_0 tRNA
Seems like you could just use sed for this:
sed -r 's/^([ACGT0-9_]+).*XF:Z:([[:alnum:]]+).*/\1\t\2/' file
This captures the part at the start of the line and the alphanumeric part following XF:Z: and outputs them, separated by a tab character. One potential advantage of this approach is that it will work independently of the position of the XF:Z: string.
Your loop looks OK (you can use this sed command in place of the awk part) but be careful with your quotes. " should be used, not “/”.
Alternatively, if you prefer awk (and assuming that the bit you're interested in is always part of the last field), you can use a custom field separator:
awk -F'[[:space:]](XF:Z:)?' -v OFS='\t' '{print $1, $NF}' file
This optionally adds the XF:Z: part to the field separator, so that it is removed from the start of the last field.
You can try, if column with "XF:Z:" is always at the end
awk 'BEGIN{OFS="\t"}{n=split($NF,a,":"); print $1, a[n]}' file.sam
you get,
AACAGATGATGAACTTATTGACGGGCGGACAGGAACTGTGTGCTGATTGTC_11 SNORD43
GTTTCCTTAGTGTAGCGGTTATCACATTCGCCT_0 tRNA
TCGACTCCCGGTGTGGGAACC_0 tRNA
or, if this column is a variable position for each file
awk 'BEGIN{OFS="\t"}
FNR==1{
for(i=1;i<=NF;i++){
if($i ~ /^XF:Z:/) break
}
}
{n=split($i,a,":"); print $1, a[n]}' file.sam
I cannot solve a very simple problem. My data file looks like:
Crap Crap 0.123456789D+09 Crap Crap
Crap Crap 0.123456798D+09 Crap Crap
I need to use AWK to subtract the number in the third column; the SECOND row minus the FIRST row.
I tried:
cat crap.txt | awk '{ A[NR-1] = $3 } END { print A[1] - A[0] }'
to no success. Maybe the format of the number is wrong? (Can AWK read scientific notation with D instead of E?)
Help!
EDIT:
Just so the community knows, AWK does not understand scientific notation which uses D instead of E (like many Fortran outputs produce). It is necessary to replace the D for E and then carry on any mathematical operation.
You could change the notation on the fly...
cat crap.txt | awk '{ sub(/D/,"E",$3); A[NR-1] = $3; } END { print A[1] - A[0] }'
awk cannot read D-notation (what does it mean by the way?). Here is an example:
printf "1.2D+1\n1.2E+1\n12\n" | awk '{ print $1/3; }'
0.4
4
4
The first one is wrong.