I have a file that I need to extract segments from based on a character range given in another file. I would like to do it using an awk command.
File one would look like this ( a single line):
AATTGTGAAGGTAGATGGCTCGCTCCGCGGCGGGGCGCGCGCGCGCGCGCGGGCTCGCTATATAGAGATATATGCGCGCGGCGCGCGGCGCGCGCGGCGCGCGCGTATATATATAGGCGCGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCCCCCCCCCCC
The second file would look like follows:
5 10
13 20
22 24
and the output would be:
GTGAAG
AGATGGCT
GCT
This one-liner will solve your problem:
awk 'BEGIN{getline sequence < "first_file"} {print substr(sequence, $1, $2 - $1 + 1) }' second_file
Explanation: This script reads string sequence from file named first_file(adjust it to the actual file name) using getline function. Then for each line of second file(which contains ranges for processing) it extracts necessary substring using substr function. substr accepts three parameters: string(sequence), position($1), and length($2 - $1 + 1).
Nya gave you the awk solution, here's one based on coreutils.
string
AATTGTGAAGGTAGATGGCTCGCTCCGCGGCGGGGCGCGCGCGCGCGCGCGGGCTCGCTATATAGAGATATATGCGCGCGGCGCGCGGCGCGCGCGGCGCGCGCGTATATATATAGGCGCGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCCCCCCCCCCC
offlen
5 10
13 20
22 24
You can get the output you want with:
while read off len; do cut -c${off}-${len} string; done < offlen
Output:
GTGAAG
AGATGGCT
GCT
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 with 2 columns. In the first column, there are several strings (IDs) and in the second values. In the strings, there are a number of dots that can be variable. I would like to split these strings based on the last dot. I found in the forum how remove the last past after the last dot, but I don't want to remove it. I would like to create a new column with the last part of the strings, using bash command (e.g. awk)
Example of strings:
5_8S_A.3-C_1.A 50
6_FS_B.L.3-O_1.A 20
H.YU-201.D 80
UI-LP.56.2011.A 10
Example of output:
5_8S_A.3-C_1 A 50
6_FS_B.L.3-O_1 A 20
H.YU-201 D 80
UI-LP.56.2011 A 10
I tried to solve it by using the following command but it works if I have just 1 dot in the string:
awk -F' ' '{{split($1, arr, "."); print arr[1] "\t" arr[2] "\t" $2}}' file.txt
You may use this sed:
sed -E 's/^([[:blank:]]*[^[:blank:]]+)\.([^[:blank:]]+)/\1 \2/' file
5_8S_A.3-C_1 A 50
6_FS_B.L.3-O_1 A 20
H.YU-201 D 80
UI-LP.56.2011 A 10
Details:
^: Start
([[:blank:]]*[^[:blank:]]+): Capture group #2 to match 0 or more whitespaces followed by 1+ non-whitespace characters.
\.: Match a dot. Since this regex pattern is greedy it will match until last dot
([^[:blank:]]+): Capture group #2 to match 1+ non-whitespace characters
\1 \2: Replacement to place a space between capture value #1 and capture value #2
Assumptions:
each line consists of two (white) space delimited fields
first field contains at least one period (.)
Sticking with OP's desire (?) to use awk:
awk '
{ n=split($1,arr,".") # split first field on period (".")
pfx=""
for (i=1;i<n;i++) { # print all but the nth array entry
printf "%s%s",pfx,arr[i]
pfx="."}
print "\t" arr[n] "\t" $2} # print last array entry and last field of line
' file.txt
Removing comments and reducing to a one-liner:
awk '{n=split($1,arr,"."); pfx=""; for (i=1;i<n;i++) {printf "%s%s",pfx,arr[i]; pfx="."}; print "\t" arr[n] "\t" $2}' file.txt
This generates:
5_8S_A.3-C_1 A 50
6_FS_B.L.3-O_1 A 20
H.YU-201 D 80
UI-LP.56.2011 A 10
With your shown samples, here is one more variant of rev + awk solution.
rev Input_file | awk '{sub(/\./,OFS)} 1' | rev
Explanation: Simple explanation would be, using rev to print reverse order(from last character to first character) for each line, then sending its output as a standard input to awk program where substituting first dot(which is last dot as per OP's shown samples only) with spaces and printing all lines. Then sending this output as a standard input to rev again to print output into correct order(to remove effect of 1st rev command here).
$ sed 's/\.\([^.]*$\)/\t\1/' file
5_8S_A.3-C_1 A 50
6_FS_B.L.3-O_1 A 20
H.YU-201 D 80
UI-LP.56.2011 A 10
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($0,n)}' file
ACCTAGAAGGATATGCGCTTGCGCGTTAGA GATCACTAGAGCTAAGGAATTTGAGATTACAGTAAGCTATGATCC
/AAAAEEEEEEEEEEAAEEEAEEEEEEEEE EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
I assumed your file is in this format
dummy header line to be ignored
ACCTAGAAGGATATGCGCTTGCGCGTTAGAGATCACTAGAGCTAAGGAATTTGAGATTACAGTAAGCTATGATCC
+
/AAAAEEEEEEEEEEAAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
000Bxxxxx111118064085vxas - header
10000000001000000000053009-000000000053009-
10000000005000000000000000+000000000000000+
10000000030000000004025404-000000004025404-
10000000039000000000004930-000000000004930-
10000000088000005417665901-000005417665901-
90000060883328364801913 - trailer
In the above file we have header and trailer and the records which start with 1 is the detail record
in the detail record,want to sum the values starting from position 28 till 44 including the sign using awk/sed command
Here is sed, with help from bc to do the arithmetic:
sed -rn '
/header|trailer/! {
s/[[:digit:]]*[+-]([[:digit:]]+)([+-])$/\2\1/
H
}
$ {
x
s/\n//gp
}
' file | bc
I assume the +/- sign follows the number.
Using awk we can solve this problem making use of substr:
substr(s, m[, n ]):
Return the at most n-character substring of s that begins at position m, numbering from 1. If n is omitted, or if n specifies more characters than are left in the string, the length of the substring shall be limited by the length of the string s.
This allows us to take the string which represents the number. Here, I assumed that the sign before and after the number is same and thus the sign of the number :
$ echo "10000000001000000000053009-000000000053009-" \
| awk '{print length($0); print substr($0,27,43-27)}'
43
-000000000053009
Since awk implicitly converts strings to numbers if you do numeric operations on them we can write the following awk-code to achieve the requested :
$ awk '/header|trailer/{next}
{s+=substr($0,27,43-27)}
END{print s}' file.dat
-5421749244
Or in a single line:
$ awk '/header|trailer/{next}{s+=substr($0,27,43-27)} END{print s}' file.dat
-5421749244
The above examples just work on the example file given by the OP. However, if you have a file containing multiple blocks with header and trailer and you only want to use the text inside these blocks (exclude everything outside of the blocks), then you should handle it a bit differently :
$ awk '/header/{s=0;c=1;next}
/trailer/{S+=s;c=0;next}
c{s+=substr($0,27,43-27)}
END{print S}' file.dat
Here we do the following:
If a line with header is found, reset the block sum s to ZERO and set c=1 indicating that we take the next lines into account
If a line with trailer is found, add the block sum s to the overall sum S and set c=0 indicating to ignore the lines.
If c/=0 compute the block sum s
At the END, print the total sum S
I have a file and a field is a time stamp like 20141028 20:49:49, I want to get the hour 20, so I use the system command :
hour=system("date -d\""$5"\" +'%H'")
the time stamp is the fifth field in my file so I used $5. But when I executed the program I found the command above just output 20 and return 0 so hour is 0 but not 20, so my question is how to get the hour in the time stamp ?
I know a method which use split function two times like this:
split($5, vec, " " )
split(vec[2], vec2, ":")
But this method is a little inefficient and ugly.
so are there any other solutions? Thanks
Another way using gawk:
gawk 'match($5, " ([0-9]+):", r){print r[1]}' input_file
If you want to know how to manage externall process output in awk:
awk '{cmd="date -d \""$5"\" +%H";cmd|getline hour;print hour;close(cmd)}' input_file
You can use the substr function to extract the hour without using system command.
for example:
awk {'print substr("20:49:49",1,2)}'
will produce output as
20
Or more specifically as in question
$ awk {'print substr("20141028 20:49:49",10,2)}'
20
substr(str, pos, len) extracts a substring from str at position pos and lenght len
if the value of $5 is 20141028 20:49:49,
$ awk {'print substr($5,10,2)}'
20