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# 1  
Old 01-18-2015
awk help
i am newbie in awk and bioinformatics.

i have a tab deliminated text file. the format is as follows. 3 records, 4 fields separated by tabs
Code:
SNP 100 101 102 103
M1 a:5 b:4 a:26 b:3
M2 a:4 b:45 a:6 b:18
M3 a:50 b:40 a:26 b:30

please help me in processing the file based on number behind the colon [:].

1) let's say, if the number after the colon [:] equal or more than 5, then just print "a" or "b"
2)if the number after the colon [:] is less than 5 then print "X".
Last edited by jim mcnamara; 01-18-2015 at 11:17 PM..
# 2  
Old 01-18-2015
Quote:
Originally Posted by jaisask
i am newbie in awk and bioinformatics.

i have a tab deliminated text file. the format is as follows. 3 records, 4 fields separated by tabs
Code:
SNP 100 101 102 103
M1 a:5 b:4 a:26 b:3
M2 a:4 b:45 a:6 b:18
M3 a:50 b:40 a:26 b:30

please help me in processing the file based on number behind the colon [:].

1) let's say, if the number after the colon [:] equal or more than 5, then just print "a" or "b"
2)if the number after the colon [:] is less than 5 then print "X".
You say you have 3 input records and show us 4 input lines???

You say your input fields are tab delimited, but there are no tabs in your sample input???

The description isn't at all clear as to what your desired output should be. From your description it could easily be:
Code:
SNP 100 101 102 103
M1 a X a X
M2 X b a b
M3 a b a b

or:
Code:
a
X
a
X
X
b
a
b
a
b
a
b

or:
Code:
a X a X
X b a b
a b a b

Please give us a clear description of what you are trying to do.

Unless the output you want looks like the 2nd sample above, what delimiter should be used between fields in the output (or does it matter)?

Please show us what you have tried (even if it isn't working).
# 3  
Old 01-18-2015
Sorry. there are 4 input lines (and 5 fields) and i want to keep header line (first line). the output should be look like:

Code:
SNP 100 101 102 103
M1 a X a X
M2 X b a b
M3 a b a b


i am still in learning process and therefore, it,s hard for me to code.


please let me know awk code for converting

Code:
SNP 100 101 102 103
M1 a:5 b:4 a:26 b:3
M2 a:4 b:45 a:6 b:18
M3 a:50 b:40 a:26 b:30


to

Code:
SNP 100 101 102 103 
M1 a X a X
M2 X b a b
M3 a b a b



Thanks
Last edited by Scrutinizer; 01-19-2015 at 12:02 AM.. Reason: Removed spurious formatting; introduced code tags
# 4  
Old 01-19-2015
Hello jaisask,

Kindly use code tags in codes/inputs/commands used in your posts as per forum rules, following may help you in same.
Code:
awk '{for(i=2;i<=NF;i++){if($i ~ /:/){A=B=$i;sub(/.*:/,X,A);sub(/:.*/,Y,B);$i=A>=5?B:"X"}}} 1'  Input_file

Output will be as follows.
Code:
SNP 100 101 102 103
M1 a X a X
M2 X b a b
M3 a b a b


EDIT: Adding a non oneliner form of solution.
Code:
awk '   {
                for(i=2;i<=NF;i++)
        {
                if($i ~ /:/)
                                {
                                        A=B=$i;
                                        sub(/.*:/,X,A);
                                        sub(/:.*/,Y,B);
                                        $i=A>=5?B:"X"
                                }
        }
        }
   1' Input_file


Thanks,
R. Singh
Last edited by RavinderSingh13; 01-19-2015 at 12:52 AM.. Reason: Added a non one liner form of solution
This User Gave Thanks to RavinderSingh13 For This Post:
jaisask
# 5  
Old 01-19-2015
Building on something that Jim McNamara posted earlier (and deleted when the output format was questioned), you could also try:
Code:
awk '
#BEGIN {	OFS = "\t"
#}
#NR == 1 {
#	$1 = $1		# reset field separators
#}
NR > 1 {for(i = 2; i <= NF; i++) { 
		p = index($i, ":")
		if(p > 0)
			if(substr($i, p + 1) +0 >= 5 )
				$i = substr($i, 1, 1)
			else	$i = "X"
	}
}
1' file

If you want tabs as output field separators instead of spaces (as originally indicated), remove the comment characters marked in red.

If you want to try this on a Solaris/SunOS system, change awk to /usr/xpg4/bin/awk, /usr/xpg6/bin/awk, or nawk.

As shown above, the output produced by your sample input is:
Code:
SNP 100 101 102 103
M1 a X a X
M2 X b a b
M3 a b a b

with the comments turned into live code, the output is:
Code:
SNP	100	101	102	103
M1	a	X	a	X
M2	X	b	a	b
M3	a	b	a	b

This User Gave Thanks to Don Cragun For This Post:
jaisask
 
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