The code you showed us seems like it would produce the desired number of additions to your field #9, but would omit the desired question marks and just append = to each subfield. The code to which you appended the comment:
I forgot that I changed the sub(/$/, ":p=", NM[i]) # add :p. to end off each NM[i] before the to sub(/$/, ":p=?", NM[i]) # add :p. to end off each NM[i] before the
However the :p.=? seemed to be iterating based on the number of splits. Maybe it is the wrong terminology but I didn't understand why, no matter what I tried. Thank you for the correction on the array being a string, I was confused.
awk
Code:
awk '
BEGIN { FS=OFS="\t" } # define FS and OFS as tab and start processing
$9 ~ /NM/ { # look for pattern NM in $9
# split $9 by ";" and cycle through them
out=""
i=split($9,NM,/;/)
for (n=1; n<=i; n++) {
sub(/$/, ":p=", NM[i]) # add :p. to end off each NM[i] before the ;
out = (out=="" ? "" : out";") NM[i]
}
$9 = out
}1' file
R_Index Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene Inheritance ExonicFunc.refGene AAChange.refGene
1 chr1 155870416 155870416 G A splicing RIT1 NM_006912:exon6:c.430-7C>T:p=;NM_006912:exon6:c.430-7C>T:p=:p=;NM_006912:exon6:c.430-7C>T:p=:p=:p=
9 chr10 112760138 112760138 A - splicing SHOC2 NM_001269039:exon2:c.704-35A>-:p=;NM_001269039:exon2:c.704-35A>-:p=:p=
11 chr18 53070914 53070914 G A exonic TCF4 .AD nonsynonymous SNV TCF4:NM_001243232:exon1:c.32C>T:p.A11V;TCF4:NM_001306208:exon1:c.32C>T:p.A11V
In rdrtx1 awk is the below close?
Code:
awk '
BEGIN { FS=OFS="\t" } # define FS and OFS as tab and start processing
$9 ~ /NM/ { # look for pattern NM in $9
gsub(";", ":p=?;", $9); # split by ; in $9
sub("$", ":p=?", $9); # add :p=? to end of each split by ;
} 1' file # update input
Hi there, I have a csv file with some columns comma sepated like this :
4502-17,PETER,ITA2,LEGUE,92,ME - HALF,23/05/10 15:00
4502-18,CARL,ITA2,LEGUE,96,ME - HALF,20/01/09 14:00
4502-19,OTTO,ITA2,LEGUE,97,ME - MARY,23/05/10 15:00
As you can see the column n. 7 is a timestamp column, I need... (23 Replies)
Hi, all
I need to get fields in a line that are separated by commas, some of the fields are enclosed with double quotes, and they are supposed to be treated as a single field even if there are commas inside the quotes.
sample input:
for this line, 5 fields are supposed to be extracted, they... (8 Replies)
Dear All,
I would like to add values of a field, if the lines match in a certain field. Then I would like to divide the sum though the number of lines that have a matched field. This is the Input:
Input:
Test1 5
Test1 10
Test2 2
Test2 5
Test2 13
Test3 4
Output:
Test1 7.5
Test1 7.5... (6 Replies)
First, thanks for the help in previous posts... couldn't have gotten where I am now without it!
So here is what I have, I use AWK to match $1 and $2 as 1 string in file1 to $1 and $2 as 1 string in file2. Now I'm wondering if I can extend this AWK command to incorporate the following:
If $1... (4 Replies)
Can someone please assist me, I'm trying to get vi to remove all the occurences of the text in a file i.e. "DEVICE=/dev/mt??". The "??" represents a number variable. Is there a globel search and delete command that I can use?
Thank You in Advance. (3 Replies)
I am trying to parse the input in awk to include the |gc= in $4 but am not able to. The below is close:
awk so far:
awk '{sub(/\|]+]++/, ""); print }' input.txt Input
chr1 955543 955763 AGRN-6|pr=2|gc=75 0 +
chr1 957571 957852 AGRN-7|pr=3|gc=61.2 0 +
chr1 970621 ... (7 Replies)
In file1 field $18 is removed.... column header is "Otherinfo", then each line in file1 is used to search file2 for a match. When a match is found the last four strings in file2 are copied to file1.
Maybe:
cut -f1-17 file1 and then match each line to file2
file1
Chr Start End ... (6 Replies)
In the awk below I am trying to set/update the value of $14 in file2 in
bold, using the matching NM_ in $12 or $9 in file2
with the NM_ in $2 of file1.
The lengths of $9 and $12 can be variable but what is consistent is the start pattern
will always be NM_ and the end pattern is always ;... (2 Replies)
The awk below produces the current output, which will add +1 to $3. However, I am trying to add the length of the matching characters between $5 and $6 to $3. I have tried using sub as a variable to store the length but am not able to do so correctly. I added comments to each line and the... (4 Replies)
The awk below executes as expected if the id in $4 (like in f) is unique. However most of my data is like f1 where the same id can appear multiple times. I think that is the reason why the awk is not working as expected. I added a comment on the line that I can not change without causing the script... (6 Replies)
Discussion started by: cmccabe
6 Replies
LEARN ABOUT SUSE
igawk
IGAWK(1) Utility Commands IGAWK(1)NAME
igawk - gawk with include files
SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ...
igawk [ all gawk options ] [ -- ] program-text file ...
DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1).
AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like
@include getopt.awk
in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path.
OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports.
EXAMPLES
cat << EOF > test.awk
@include getopt.awk
BEGIN {
while (getopt(ARGC, ARGV, "am:q") != -1)
...
}
EOF
igawk -f test.awk
SEE ALSO gawk(1)
Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995.
AUTHOR
Arnold Robbins (arnold@skeeve.com).
Free Software Foundation Nov 3 1999 IGAWK(1)
01-23-2018
.
= to each subfield. The code to which you appended the comment: