Yes, I want to append to the same list (rather than over-writing), and I'm not sure how to do that.
Also, I want this to loop so that it starts again at the new line 1 once the original line 1 (plus any other lines containing the exclusion) has been removed.
If $3 > $4, print $2 (ID2) > exclusionlist.txt # This one will create or if exist,overwrite
If $3 < $4, print $1 (ID1)>> exclusionlist.txt # Then here you append...
If $3==$4 && $5 < $6, print $2 (ID2) >> exclusionlist.txt
If $3==$4 && $5 > $6, print $1 (ID1) >> exclusionlist.txt
Let me paraphrase your request: You select either of the IDs in field1 or 2 depending on conditions in the rest of the line, and then remove all occurrences of the selected ID in the rest of the file. Do you HAVE to populate the exclusion file, i.e. do you need it afterwards? Or would a single pass operation be sufficient, removing ALL the applicable IDs?
Yes, your interpretation is correct, and it is vitally important that I populate an exclusion file. The original file itself should eventually grind itself down to 0 lines, and it is the the exclusion file that I am interested in.
My latest attempt is as follows (it involves having to rename file.txt to 1.txt):
Due to my poor scripting skills, I am having to: (1) rename my file after each loop in order for it to be continuously executed, and (2) ending up with a new exclusion list per loop, rather than a single 'master' exclusion list - I can easily concatenate them all at the end, so this is not a major problem, but it's messy.
The problem I have when I execute this script is that it seems to scan through the whole file on the first pass (rather than just line 1), creating a long exclusion list just from the first run.
Any help/suggestions would be greatly appreciated.
Hi, I'd like to loop an action over all files with given extension within a folder.
The "main" action is: awk -F "\t" 'BEGIN{OFS="\t"}{if ($10=="S") print$0; }' input.txt > output.txt
The input.txt should be every file in the folder with *.subVCF extension; and the output should be a file... (3 Replies)
Dear folks
I have two data set which there names are "final.map" and "1.geno" and look like this structures:
final.map:
gi|358485511|ref|NC_006088.3| 2044
gi|358485511|ref|NC_006088.3| 2048
gi|358485511|ref|NC_006088.3| 2187
gi|358485511|ref|NC_006088.3| 17654
... (2 Replies)
Hi All,
I am new to AWK programming. I have the following for loop in my awk program.
cat printhtml.awk:
BEGIN
-------- <some code here>
END{
----------<some code here>
for(N=0; N<H; N++)
{
for(M=5; M<D; M++) print "\t" D "";
}
-----
}
... (2 Replies)
Hi ,
Please excuse me for opening a new thread i am unable to find out the syntax error
in my if else condition inside for loop in awk command ,
my actual aim is to print formatted html td tag when if condition (True) having string as "failed",
could anyone please advise what is the right... (2 Replies)
limit.csv data
--------------
5600050 38Nhava
400077 27Bomay
rate.txt data
-------------
38NhaVA
27BomaY
27Bomay
below is my script:
for i in `cat limit.csv`
do
b=`awk '{print $1}' $i` (4 Replies)
I am parsing file for the fields using awk command, first i check 26th field for two characters using substr function if it matches then using for loop on array i search 184th field for 4 chars if it matches then i print the required fields but on execution i get the error, please help...... (5 Replies)
Hello all,
Here is what my bash script does: sums number columns, saves the tot in new column, outputs if tot >= threshold val:
> cat getnon0file.sh
#!/bin/bash
this="getnon0file.sh"
USAGE=$this"
InFile="xyz.38"
Min="0.05"
#
awk '{sum=0; for(n=2; n<=NF; n++){sum+=$n};... (4 Replies)
I have two files which I would like to compare and then manipulate in a way.
File1:
pictures.txt 1.1 1.3
dance.txt 1.2 1.4
treehouse.txt 1.3 1.5
File2:
pictures.txt 1.5 ref2313 1.4 ref2345 1.3 ref5432 1.2 ref4244
dance.txt 1.6 ref2342 1.5 ref2352 1.4 ref0695 1.3 ref5738 1.2... (1 Reply)
Hello!
I've got a loop in which I am processing a list of values gotten through a file with read command.
It seems that instead of processing the lines (values) one by one, I process them all together.
the input file is:
20
20
20
80
70
70
20
The code is: (2 Replies)
