Recently, I read some hex data with 16 length, like 0x1000 0000 0000 0000, but print out some strange thing when print 0xffff ffff ffff ffff
awk '{printf("0x\n", 0x1000000000000000)}' output `0x1000000000000000` ok.
But, instead with
16 f awk '{printf("0x\n", 0xffffffffffffffff)}', output 0
15 f awk '{printf("0x\n", 0xfffffffffffffff)}', output 1000000000000000 （14 0)
15 f awk '{printf("0x\n", 0xfffffffffffffff0)}', output 0
14 f awk '{printf("0x\n", 0xffffffffffffff)}', output 100000000000000 (13 0)
14 f awk '{printf("0x\n", 0xffffffffffffff0)}', output 100000000000000 (14 0)
14 f awk '{printf("0x\n", 0xffffffffffffff00)}', output 0
13 f awk '{printf("0x\n", 0xfffffffffffff)}', output fffffffffffff （13f）
13 f awk '{printf("0x\n", 0xfffffffffffff0)}', output fffffffffffff0 （13f）
13 f awk '{printf("0x\n", 0xfffffffffffff00)}', output fffffffffffff00 （13f）
13 f awk '{printf("0x\n", 0xfffffffffffff000)}', output fffffffffffff000 （13f）
so 13f is ok, how to print 16f?
You are missing the format string in the printf() call. Note that printfworks differently than print. I assume you see some random erratic behavior of the awk interpreter.
Another typical awk problem is that it typically uses double precision floating point numbers to represent all numeric value (also integers) so you would loose precision and get strange artifacts when you get near 64 bit. This depends on the actual awk implementation.
You are probably seeing a mixture of these two problems. I admit the rounding to 0 is bizarre.
Related
I have a dataframe like this
1 3 MAPQ=0;CT=3to5;SRMAPQ=60
2 34 MAPQ=60;CT=3to5;SRMAPQ=67
4 56 MAPQ=67;CT=3to5;SRMAPQ=50
5 7 MAPQ=44;CT=3to5;SRMAPQ=61
with using awk (or others)
I want to extract rows with only SRMAPQ over 60.
This means the output is
2 34 MAPQ=60;CT=3to5;SRMAPQ=67
5 7 MAPQ=44;CT=3to5;SRMAPQ=61
update: "SRMAPQ=60" can be anywhere in the line,
MAPQ=44;CT=3to5;SRMAPQ=61;DT=3to5
You don't have to extract the value out of SRMAPQ separately and do the comparison. If the format is fixed like above, just use = as the field separator and access the last field using $NF
awk -F= '$NF > 60' file
Or if SRMAPQ can occur anywhere in the line (as updated in the comments), use a generic approach
awk 'match($0, /SRMAPQ=([0-9]+)/){ l = length("SRMAPQ="); v = substr($0, RSTART+l, RLENGTH-l) } v > 60' file
I would use GNU AWK following way let file.txt content be
1 3 MAPQ=0;CT=3to5;SRMAPQ=60
2 34 MAPQ=60;CT=3to5;SRMAPQ=67;SOMETHING=2
4 56 MAPQ=67;CT=3to5;SRMAPQ=50
5 7 MAPQ=44;CT=3to5;SRMAPQ=61
then
awk 'BEGIN{FS="SRMAPQ="}$2>60' file.txt
output
2 34 MAPQ=60;CT=3to5;SRMAPQ=67;SOMETHING=2
5 7 MAPQ=44;CT=3to5;SRMAPQ=61
Note: added SOMETHING to test if it would work when SRMAPQ is not last. Explantion: I set FS to SRMAPQ= thus what is before that becomes first field ($1) and what is behind becomes second field ($2). In 2nd line this is 67;SOMETHING=2 with which GNU AWK copes by converting its' longmost prefix which constitute number in this case 67, other lines have just numbers. Disclaimer: this solution assumes that all but last field have trailing ;, if this does not hold true please test my solution fully before usage.
(tested in gawk 4.2.1)
I have a file where the data looks like:
sp_0005_SySynthetic ConstructTumor protein p53 N-terminal transcription-activation domain
A=9 C=2 D=3 E=4 F=2 G=15 I=3 K=3 L=9 M=3 N=5 P=2 Q=11 R=8 S=12 T=6 V=8 W=1 Y=5
Amino acid alphabet = 19
Sequence length = 115
sp_0017_CaCamelidSorghum bicolor multidrug and toxic compound extrusion sbmate
A=10 C=2 D=4 E=4 F=2 G=15 H=1 I=2 K=4 L=7 M=2 N=5 P=3 Q=6 R=4 S=18 T=7 V=10 W=5 Y=10
Amino acid alphabet = 20
Sequence length = 126
sp_0021_LgLlamabotulinum neurotoxin BoNT serotype F
A=14 C=2 D=4 E=5 F=4 G=15 I=2 K=3 L=6 M=2 N=6 P=4 Q=7 R=8 S=13 T=10 V=8 W=3 Y=10
Amino acid alphabet = 19
Sequence length = 131
I want to extract the vales of 'Amino acid alphabet' and 'Sequence length into an output file', and it should look like:
19 115
20 126
19 131
As I am new to bash, all I could try so far is:
grep -i "Amino acid alphabet = $i" test.txt >>out.txt
But, I don't want the word "Amino acid alphabet" in the output. I only want the values of "Amino acid alphabet" and "Sequence length" as two columns.
Can I get any help how to do that? Thanks in advance.
$ awk -v RS= '{print $(NF-4), $NF}' file
19 115
20 126
19 131
Assuming both fields exist for all your records:
awk '/^Amino acid alphabet/{printf $NF FS} /^Sequence length/{print $NF}' file
19 115
20 126
19 131
Also you may want to have some introduction about awk into the awk wiki
This code: grep -i "Amino acid alphabet = $i" test.txt >>out.txt includes the shell expansion of $i. If you have not given a value to i then the search pattern resolves to Amino acid alphabet = , and thus will find each line that contains that. The $i would change the search pattern if $i had a value.
There are many ways to get what you want with BASH. one is to use grep with PCRE (Perl-style) regex enabled:
grep -Po "(?<=Amino acid alphapbet = )\d+" test.txt >> out.text
#yields:
19
20
19
(?<=string) tells grep that for the rest to match, it must have been preceded by string, but string is not a part of the Match. -Po are the options to enable PCRE (Perl Style) and to only print the match, rather than the whole line in which there was a match.
Note that the output redirect is >> if you want to append to a file if it already contains lines, > will overwrite an existing file if it exists, (without asking for confirmation!)
sed can do this too.
sed -En '/^Amino acid alphabet =/h; /^Sequence length =/{ H; x; s/[^0-9]+/ /g; s/^ //; p; }' infile > outfile
/^Amino acid alphabet =/h stores the first line in the save buffer.
/^Sequence length =/{ triggers all the steps inside the curlies.
H adds the current line to the save buffer.
x swaps the save buffer back to the workspace.
s/[^0-9]+/ /g; changes every sequence on NON-digits to a single space.
This includes the newline.
s/^ //; removes the leading space.
p prints the output line for this data set.
Assume the following file
#zvview.exe
#begin Present/3
77191.0000 189.320100 0 0 3 0111110 16 1
-8.072430+6-8.072430+6 77190 0 1 37111110 16 2
37 2 111110 16 3
8.115068+6 0.000000+0 8.500000+6 6.390560-2 9.000000+6 6.803440-1111110 16 4
9.500000+6 1.685009+0 1.000000+7 2.582780+0 1.050000+7 3.260540+0111110 16 5
37 2 111110 16 18
What I would like to do, is print in two columns, the fields after line 6. This can be done using NR. The tricky part is the following : Every second field, should go in one column as well as adding an E before the sign, so that the output file will look like this
8.115068E+6 0.000000E+0
8.500000E+6 6.390560E-2
9.000000E+6 6.803440E-1
9.500000E+6 1.685009E+0
1.000000E+7 2.582780E+0
1.050000E+7 3.260540E+0
From the output file you see that I want to keep in $6 only length($6)=10 characters.
How is it possible to do it in awk?
can do all in awk but perhaps easier with the unix toolset
$ sed -n '6,7p' file | cut -c2-66 | tr ' ' '\n' | pr -2ats' '
8.115068+6 0.000000+0
8.500000+6 6.390560-2
9.000000+6 6.803440-1
9.500000+6 1.685009+0
1.000000+7 2.582780+0
1.050000+7 3.260540+0
Here is a awk only solution or comparison
$ awk 'NR>=6 && NR<=7{$6=substr($6,1,10);
for(i=1;i<=6;i+=2) {f[++c]=$i;s[c]=$(i+1)}}
END{for(i=1;i<=c;i++) print f[i],s[i]}' file
8.115068+6 0.000000+0
8.500000+6 6.390560-2
9.000000+6 6.803440-1
9.500000+6 1.685009+0
1.000000+7 2.582780+0
1.050000+7 3.260540+0
Perhaps shorter version,
$ awk 'NR>=6 && NR<=7{$6=substr($6,1,10);
for(i=1;i<=6;i+=2) print $i FS $(i+1)}' file
8.115068+6 0.000000+0
8.500000+6 6.390560-2
9.000000+6 6.803440-1
9.500000+6 1.685009+0
1.000000+7 2.582780+0
1.050000+7 3.260540+0
to convert format to standard scientific notation, you can pipe the result to
sed or embed something similar in awk script (using gsub).
... | sed 's/[+-]/E&/g'
8.115068E+6 0.000000E+0
8.500000E+6 6.390560E-2
9.000000E+6 6.803440E-1
9.500000E+6 1.685009E+0
1.000000E+7 2.582780E+0
1.050000E+7 3.260540E+0
With GNU awk for FIELDWIDTHS:
$ cat tst.awk
BEGIN { FIELDWIDTHS="9 2 9 2 9 2 9 2 9 2 9 2" }
NR>5 && NR<8 {
for (i=1;i<NF;i+=4) {
print $i "E" $(i+1), $(i+2) "E" $(i+3)
}
}
$ awk -f tst.awk file
8.115068E+6 0.000000E+0
8.500000E+6 6.390560E-2
9.000000E+6 6.803440E-1
9.500000E+6 1.685009E+0
1.000000E+7 2.582780E+0
1.050000E+7 3.260540E+0
If you really want to get rid of the leading blanks then there's various ways to do it (simplest being gsub(/ /,"",$<field number>) on the relevant fields) but I left them in because the above allows your output to line up properly if/when your numbers start with a -, like they do on line 4 of your sample input.
If you don't have GNU awk, get it as you're missing a LOT of extremely useful functionality.
I tried to combine #karafka 's answer using substr, so the following does the trick!
awk 'NR>=6 && NR<=7{$6=substr($6,1,10);for(i=1;i<=6;i+=2) print substr($i,1,8) "E" substr($i,9) FS substr($(i+1),1,8) "E" substr($(i+1),9)}' file
and the output is
8.115068E+6 0.000000E+0
8.500000E+6 6.390560E-2
9.000000E+6 6.803440E-1
9.500000E+6 1.685009E+0
1.000000E+7 2.582780E+0
1.050000E+7 3.260540E+0
I have large tab delimited file with 1000 columns. I want to rearrange so that certain columns have to be moved to the end.
Could anyone help using awk
Example input:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Move columns 5,6,7,8 to the end.
Output:
1 2 3 4 9 10 11 12 13 14 15 16 17 18 19 20 5 6 7 8
This prints columns 1 to a, then b to the last, and then columns a+1 to b-1:
$ awk -v a=4 -v b=9 '{for (i=1;i<=NF;i+=i==a?b-a:1) {printf "%s\t",$i};for (i=a+1;i<b;i++) {printf "%s\t",$i};print""}' file
1 2 3 4 9 10 11 12 13 14 15 16
17 18 19 20 5 6 7 8
The columns are moved in this way for every line in the input file, however many lines there are.
How it works
-v a=4 -v b=9
This defines the variables a and b which determine the limits on which columns will be moved.
for (i=1;i<=NF;i+=i==a?b-a:1) {printf "%s\t",$i}
This prints all columns except the ones from a+1 to b-1.
In this loop, i is incremented by one except when i==a in which case it is incremented by b-a so as to skip over the columns to be moved. This is done with awk's ternary statement:
i += i==a ? b-a : 1
+= simply means "add to." i==a ? b-a : 1 is the ternary statement. The value that it returns depends on whether i==a is true or false. If it is true, the value before the colon is returned. If it is false, the value after the colon is returned.
for (i=a+1;i<b;i++) {printf "%s\t",$i}
This prints columns a+1 to b-1.
print""
This prints a newline character to end the line.
Alternative solution that avoids printf
This approach assembles the output into the variable out and then prints with a plain print command, avoiding printf and the need for percent signs:
awk -v a=4 -v b=9 '{out="";for (i=1;i<=NF;i+=i==a?b-a:1) out=out $i"\t";for (i=a+1;i<b;i++) out=out $i "\t";print out}' file
One way to rearrange 2 columns ($5 become $20 and $20 become $5) the rest stay unchanged :
$ awk '{x=$5; $5=$20; $20=x; print}' file.txt
for 4 columns :
$ awk '{
x=$5; $5=$20; $9=x;
y=$9; $9=$10; $10=y;
print
}' file.txt
My approach:
awk 'BEGIN{ f[5];f[6];f[7];f[8] } \
{ for(i=1;i<=NF;i++) if(!(i in f)) printf "%s\t", $i; \
for(c in f) printf "%s\t", $c; printf "\n"} ' file
It's splitted in 3 parts:
The BEGIN{} part determines which field should be moved to the end. The indexes of the array f are moved. In the example it's 5, 6, 7 and 8.
Cycle trough every field (doesn't matter if there are 1000 fields or more) and check if they are in the array. If not print them.
Now we need the skipped fields. Cycle trough the f array and print those values.
Another way in awk
Switch last A-B with last N fields
awk -vA=4 -vB=8 '{x=B-A;for(i=A;i<=B;i++){y=$i;$i=$(t=(NF-x--));$t=y}}1' file
Put N rows from end into positon A
awk -vA=3 -vB=8 '{split($0,a," ");x=A++;while(x++<B)$x=a[NF-(B-x)];while(B++<NF)$B=a[A++]}1' file
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