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 to abort. Each line in f2 is searched and must contain the id, in this case COL1A2 but that id may not be a single entry. That is the id may appear 5 times, but each line with that is in f2 is searched. Using the $4 in f1 as the id and reading each $1, $2, and $3 value into a variable min and max.
The $4 is then split on the _ in f2 and read into array. The same id from f1 may appear in multiple lines of f2 however each will have unique $2 and $3 values. Each value in the split will match a $4 id in f1. The min and max must match the $1 of f2 and be between the $2 and $3 values in f2. An exact match is not needed rather just that the min or max variables falls within $2 and $3. If that is true then exon is printed in $5 of f2 if it is not true then intron is printed in $5. Most of this works as expected I just did not account for the possibity for multiple enteries and am nut sure how to adjust for it. Thank you
For example using the contents of the f1 where COL1A2 appears 3 times, each entry or line is searched in f2. Currently, I believe since COL1A2 is not unique not match is found in f2 as the min and max are not set per entry or line. Thank you .
hello experts,
I have a file: File1 Sample Test1
This is a Test
Sample Test2
Another Test
Final Test3
A final Test
I can use sed to delete the line with specific text
ie: sed '/Test2/d' File1.txt > File2.txt
How can I delete the line with the matching text and the line immediately... (6 Replies)
Hi,
I wish to use a column, as inputted by a user from command line, for pattern matching.
awk file:
{
if($1 ~ /^8/)
{
print $0> "temp2.csv"
}
}
something like this, but i want '$1' to be any column as selected by the user from command line.
... (1 Reply)
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)
Sample file:
This is line one,
this is another line,
this is the PRIMARY INDEX line
l ;
This is another line
The command should find the line with “PRIMARY INDEX” and remove the last character from the line preceding it (in this case , comma) and remove the first character from the line... (5 Replies)
Hi,
I want to achieve something similar to what described in another post:
The difference is I want to add the line if the pattern is not found.
File 1:
A123, valueA, valueB
B234, valueA, valueB
C345, valueA, valueB
D456, valueA, valueB
E567, valueA, valueB
F678, valueA, valueB
... (11 Replies)
Hi there,
I'm trying to use awk to print out the entire line that contains a match to a certain regex and then append some text,plus the match to the end of the line.
So far I have:
awk -F: '{print "RG:Z:" $2}' file
Which prints out the match I want plus the additional text, but I'm stuck... (3 Replies)
Hello Help,
2356798 7689867 999 000
123678 20385907 9797 666
17978975 87468976 968978 98798
I am trying to have out put which actually look for the third column value of 9797 and then it insert line there after with first, second column value exactly as the previous line and replace the third... (3 Replies)
The bash bash below extracts the oldest folder from a directory and stores it in filename
That result will match a line in bold in input. In the matching line there is an_xxx digit in italics that
(once the leading zero is removed) will match a line in link. That is the lint to print in output.... (2 Replies)
In the awk I am trying to add :p.=? to the end of each $9 that matches the pattern NM_. The below executes andis close but I can not seem to figure out why the :p.=? repeats in the split as in the green in the current output. I have added comments as well. Thank you :).
file
... (4 Replies)
In the awk below I am trying to cp and paste each matching line in f2 to $3 in f1 if $2 of f1 is in the line in f2 somewhere. There will always be a match (usually more then 1) and my actual data is much larger (several hundreds of lines) in both f1 and f2. When the line in f2 is pasted to $3 in... (4 Replies)