take out specific columns from mulitple files - awk

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

Related

How do I print every nth entry of the mth column, starting from a particular line of a file?

Consider the following data in a file file.txt:
$
$
$
FORCE 10 30 40
* 1 5 4
FORCE 11 20 22
* 2 3 0
FORCE 19 25 10
* 16 12 8
.
.
.
I want to print every 2nd element of the third column, starting from line 4, resulting in:
30
20
25
I have tried:
cat file.txt | sed 's/\|/ /' | awk 'NR%2==4 {print $3}'
However, this is not resulting in anything being printed and no errors generated either.
You might use awk checking that the row number > 3 and then check for an even row number with NR%2==0.
Note that you don't have to use cat
awk 'NR > 3 && NR%2==0 {
print $3
}' file.txt
Output
30
20
25
Using sed
$ sed -En '4~2s/([^ \t]*[ \t]+){2}([^ \t]*).*/\2/p' input_file
30
20
25
I have tried:
cat file.txt | sed 's/\|/ /' | awk 'NR%2==4 {print $3}'
However, this is not resulting in anything being printed and no errors
generated either.
You do not need cat whilst using GNU sed as it can read file on its' own, in this case it would be sed 's/\|/ /' file.txt.
You should consider if you need that part at all, your sample input does not have pipe character at all, so it would do nothing to it. You might also drop that part if lines holding values you want to print do not have that character.
Output is empty as NR%2==4 does never hold, remainder of division by x is always smaller than x (in particular case of %2 only 2 values are possible: 0 and 1)
This might work for you (GNU sed):
sed -nE '4~2s/^((\S+)\s*){3}.*/\2/p' file
Turn off implicit printing by setting the -n option and reduce back slashes in regexps by turning on -E.
From the fourth line and then every second line thereafter, capture the third column and print it.
N.B. The \2 represents the last inhabitant of that back reference which in conjunction with the {3} means the above.
Alternative:
sed -n '4,${s/^\(\(\S\+\)\s*\)\{3\}.*/\2/p;n}' file

Problems with awk substr

I am trying to split a file column using the substr awk command. So the input is as follows (it consists of 4 lines, one blank line):
#NS500645:122:HYGVMBGX2:4:21402:2606:16446:ACCTAGAAGG:R1
ACCTAGAAGGATATGCGCTTGCGCGTTAGAGATCACTAGAGCTAAGGAATTTGAGATTACAGTAAGCTATGATCC
/AAAAEEEEEEEEEEAAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
I want to split the second line by the pattern "GATC" but keeping it on the right sub-string like:
ACCTAGAAGGATATGCGCTTGCGCGTTAGA GATCACTAGAGCTAAGGAATTTGAGATTACAGTAAGCTATGATCC
I want that the last line have the same length as the splitted one and regenerate the file like:
ACCTAGAAGGATATGCGCTTGCGCGTTAGA
/AAAAEEEEEEEEEEAAEEEAEEEEEEEEE
GATCACTAGAGCTAAGGAATTTGAGATTACAGTAAGCTAT
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
GATCC
EEEEE
For split the last colum I am using this awk script:
cat prove | paste - - - - | awk 'BEGIN
{FS="\t"; OFS="\t"}\ {gsub("GATC","/tGATC", $2); {split ($2, a, "\t")};\ for
(i in a) print substr($4, length(a[i-1])+1,
length(a[i-1])+length(a[i]))}'
But the output is as follows:
/AAAAEEEEEEEEEEAAEEEAEEEEEEEEE
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
Being the second and third line longer that expected.
I check the calculated length that are passed to the substr command and are correct:
1 30
31 70
41 45
Using these length the output should be:
/AAAAEEEEEEEEEEAAEEEAEEEEEEEEE
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
EEEEE
But as I showed it is not the case.
Any suggestions?
I guess you're looking something like this, but your question formatting is really confusing
$ awk -v OFS='\t' 'NR==1 {next}
NR==2 {n=index($0,"GATC")}
/^[^+]/ {print substr($0,1,n-1),substr($0,n)}' file
ACCTAGAAGGATATGCGCTTGCGCGTTAGA GATCACTAGAGCTAAGGAATTTGAGATTACAGTAAGCTATGATCC
/AAAAEEEEEEEEEEAAEEEAEEEEEEEEE EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
I assumed your file is in this format
dummy header line to be ignored
ACCTAGAAGGATATGCGCTTGCGCGTTAGAGATCACTAGAGCTAAGGAATTTGAGATTACAGTAAGCTATGATCC
+
/AAAAEEEEEEEEEEAAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE

summarizing the contents of a text file to an other one using awk

I have a big text file with 2 tab separated fields. as you see in the small example every 2 lines have a number in common. I want to summarize my text file in this way.
1- look for the lines that have the number in common and sum up the second column of those lines.
small example:
ENST00000054666.6 2
ENST00000054666.6_2 15
ENST00000054668.5 4
ENST00000054668.5_2 10
ENST00000054950.3 0
ENST00000054950.3_2 4
expected output:
ENST00000054666.6 17
ENST00000054668.5 14
ENST00000054950.3 4
as you see the difference is in both columns. in the 1st column there is only one repeat of each common and without "_2" and in the 2nd column the values is sum up of both lines (which have common number in input file).
I tried this code but does not return what I want:
awk -F '\t' '{ col2 = $2, $2=col2; print }' OFS='\t' input.txt > output.txt
do you know how to fix it?
Solution 1st: Following awk may help you on same.
awk '{sub(/_.*/,"",$1)} {a[$1]+=$NF} END{for(i in a){print i,a[i]}}' Input_file
Solution 2nd: In case your Input_file is sorted by 1st field then following may help you.
awk '{sub(/_.*/,"",$1)} prev!=$1 && prev{print prev,val;val=""} {val+=$NF;prev=$1} END{if(val){print prev,val}}' Input_file
Use > output.txt at the end of the above codes in case you need the output in a output file too.
If order is not a concern, below may also help :
awk -v FS="\t|_" '{count[$1]+=$NF}
END{for(i in count){printf "%s\t%s%s",i,count[i],ORS;}}' file
ENST00000054668.5 14
ENST00000054950.3 4
ENST00000054666.6 17
Edit :
If the order of the output does matter, below approach using a flag helps :
$ awk -v FS="\t|_" '{count[$1]+=$NF;++i;
if(i==2){printf "%s\t%s%s",$1,count[$1],ORS;i=0}}' file
ENST00000054666.6 17
ENST00000054668.5 14
ENST00000054950.3 4

Print rows that has numbers in it

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

setting default numeric format in awk

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