Filter column with awk and regexp

Question

I\'ve a pretty simple question. I\'ve a file containing several columns and I want to filter them using awk.

So the column of interest is the 6th column and I want to fi

Answer 1

I know this thread has already been answered, but I actually have a similar problem (relating to finding strings that "consume query"). I'm trying to sum up all of the integers preceding a character like 'S', 'M', 'I', '=', 'X', 'H', as to find the read length via a paired-end read's CIGAR string.

I wrote a Python script that takes in the column $6 from a SAM/BAM file:

import sys                      # getting standard input
import re                       # regular expression module

lines = sys.stdin.readlines()   # gets all CIGAR strings for each paired-end read
total = 0
read_id = 1                     # complements id from filter_1.txt

# Get an int array of all the ints matching the pattern 101M, 1S, 70X, etc.
# Example inputs and outputs: 
# "49M1S" produces total=50
# "10M757N40M" produces total=50

for line in lines:
    all_ints = map(int, re.findall(r'(\d+)[SMI=XH]', line))
    for n in all_ints:
        total += n
    print(str(read_id)+ ' ' + str(total))
    read_id += 1
    total = 0

The purpose of the read_id is to mark each read you're going through as "unique", in case if you want to take the read_lengths and print them beside awk-ed columns from a BAM file.

I hope this helps, or at least helps the next user that has a similar issue. I consulted https://stackoverflow.com/a/11339230 for reference.

Answer 2

This should do the trick:

awk '$6~/^(([1-9]|[1-9][0-9]|100)[SM]){2}$/' file

Regexplanation:

^                        # Match the start of the string
(([1-9]|[1-9][0-9]|100)  # Match a single digit 1-9 or double digit 10-99 or 100
[SM]                     # Character class matching the character S or M
){2}                     # Repeat everything in the parens twice
$                        # Match the end of the string

---

You have quite a few issue with your statement:

awk '{ if($6 == '/[1-100][S|M][1-100][S|M]/') print} file.txt

• == is the string comparision operator. The regex comparision operator is ~.
• You don't quote regex strings (you never quote anything with single quotes in awk beside the script itself) and your script is missing the final (legal) single quote.
• [0-9] is the character class for the digit characters, it's not a numeric range. It means match against any character in the class 0,1,2,3,4,5,6,7,8,9 not any numerical value inside the range so [1-100] is not the regular expression for digits in the numerical range 1 - 100 it would match either a 1 or a 0.
• [SM] is equivalent to (S|M) what you tried [S|M] is the same as (S|\||M). You don't need the OR operator in a character class.

Awk using the following structure condition{action}. If the condition is True the actions in the following block {} get executed for the current record being read. The condition in my solution is $6~/^(([1-9]|[1-9][0-9]|100)[SM]){2}$/ which can be read as does the sixth column match the regular expression, if True the line gets printed because if you don't get any actions then awk will execute {print $0} by default.

Answer 3

Try this:

awk '$6 ~/^([1-9]|0[1-9]|[1-9][0-9]|100)+[S|M]+([1-9]|0[1-9]|[1-9][0-9]|100)+[S|M]$/' file.txt

Because you did not say exactly how the formatting will be in column 6, the above will work where the column looks like '03M05S', '40S100M', or '3M5S'; and exclude all else. For instance, it will not find '03F05S', '200M05S', '03M005S, 003M05S, or '003M005S'.

If you can keep the digits in column 6 to two when 0-99, or three when exactly 100 - meaning exactly one leading zero when under 10, and no leading zeros otherwise, then it is a simpler match. You can use the above pattern but exclude single digits (remove the first [1-9] condition), e.g.

awk '$6 ~/^(0[1-9]|[1-9][0-9]|100)+[S|M]+(0[1-9]|[1-9][0-9]|100)+[S|M]$/' file.txt

Answer 4

The way to write the script you posted:

awk '{ if($6 == '/[1-100][S|M][1-100][S|M]/') print} file.txt

in awk so it will do what you SEEM to be trying to do is:

awk '$6 ~ /^(([1-9][0-9]?|100)[SM]){2}$/' file.txt

Post some sample input and expected output to help us help you more.

Answer 5

I would do the regex check and the numeric validation as different steps. This code works with GNU awk:

$ cat data
a b c d e 132x123y
a b c d e 123S12M
a b c d e 12S23M
a b c d e 12S23Mx

We'd expect only the 3rd line to pass validation

$ gawk '
    match($6, /^([[:digit:]]{1,3})[SM]([[:digit:]]{1,3})[SM]$/, m) && 
    1 <= m[1] && m[1] <= 100 && 
    1 <= m[2] && m[2] <= 100 {
        print
    }
' data
a b c d e 12S23M

For maintainability, you could encapsulate that into a function:

gawk '
    function validate6() {
        return( match($6, /^([[:digit:]]{1,3})[SM]([[:digit:]]{1,3})[SM]$/, m) && 
                1<=m[1] && m[1]<=100 && 
                1<=m[2] && m[2]<=100 );
    }
    validate6() {print}
' data

Answer 6

Regexes cannot check for numeric values. "A number from 1 to 100" is outside what regexes can do. What you can do is check for "1-3 digits."

You want something like this

/\d{1,3}[SM]\d{1,3}[SM]/

Note that the character class [SM] doesn't have the ! alternation character. You would only need that if you were writing it as (S|M).