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awk to split file using multiple deliminators

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# 1  
Old 01-04-2017
awk to split file using multiple deliminators
I am trying to use awk to split a input file using multiple delimiters :-|. The input file is just one field and the output is 6 tab-delimited fields.

The awk below does run and works as expected until I add the third delimiter |, which gives the current output below. I am not sure what is wrong. Thank you Smilie.

input
Code:
chr1:1013574-1013576|ISG15	
chr1:1013984-1014478|ISG15
chr1:1020163-1020383|AGRN

Code:
awk -F'[:-|]' '{print $1 "\t" $2 "\t" $3 "\t" $1 ":" $2 "-" $3 "\t" "." "\t" $4}' input

desired output
Code:
chr1	1013574	1013576	chr1:1013574-1013576	.	ISG15	
chr1	1013984	1014478	chr1:1013984-1014478	.	ISG15
chr1	1020163	1020383	chr1:1020163-1020383	.	AGRN

current output
Code:
	
	                .	1
			.	1
			.	1

Last edited by cmccabe; 01-04-2017 at 11:07 AM.. Reason: fixed format
# 2  
Old 01-04-2017
Hello cmccabe,

Could you please try following and let me know if this helps you(should work if your Input_file is similar as shown sample).
Code:
awk -F"[:|-]" '{print $1 "\t" $2 OFS $3 OFS $1":"$2"-"$3 "\t" "." "\t" $NF}'  Input_file

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
cmccabe
# 3  
Old 01-04-2017
Hi,

Code:
awk -F"[|:-]" ' { print $1 "\t" $2 "\t" $3 "\t" $1 ":" $2 "-" $3 "\t" "." "\t" $4}' file

Gives the desired output:
Quote:
chr1 1013574 1013576 chr1:1013574-1013576 . ISG14
chr1 1013984 1014478 chr1:1013984-1014478 . ISG15
chr1 1020163 1020383 chr1:1020163-1020383 . AGRN
This User Gave Thanks to greet_sed For This Post:
cmccabe
# 4  
Old 01-04-2017
I added the output of both commands and seem to be having trouble with the | symbol in the input file. I tried to split on the | that and got an empty output. Thank you Smilie.

Code:
awk -F"[:|-]" '{print $1 "\t" $2 OFS $3 OFS $1":"$2"-"$3 "\t" "." "\t" $NF}' file > output

Code:
chr1    1013574 1013576;ISG15     chr1:1013574-1013576;ISG15        .    1013576;ISG15    
chr1    1013984 1014478;ISG15 chr1:1013984-1014478;ISG15    .    1014478;ISG15
chr1    1020163 1020383;AGRN chr1:1020163-1020383;AGRN    .    1020383;AGRN

Code:
awk -F"[|:-]" ' { print $1 "\t" $2 "\t" $3 "\t" $1 ":" $2 "-" $3 "\t" "." "\t" $4}' file > output2

Code:
chr1    1013574    1013576;ISG15        chr1:1013574-1013576;ISG15        .    
chr1    1013984    1014478;ISG15    chr1:1013984-1014478;ISG15    .    
chr1    1020163    1020383;AGRN    chr1:1020163-1020383;AGRN    .

Last edited by cmccabe; 01-04-2017 at 11:40 AM.. Reason: added details
# 5  
Old 01-04-2017
Hello cmccabe,

Sorry didn't get you, is your output requirement is not the very first post one? As I could see your second post is having different output expected, kindly enlighten us all for this.

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
cmccabe
# 6  
Old 01-04-2017
The desired output in post 1 is correct for some reason I am not getting that though. Maybe the original input file is corrupt, I will check. Thank you very much Smilie.

---------- Post updated at 09:50 AM ---------- Previous update was at 09:44 AM ----------

Both commands work great, sorry I had a space in the file that was causing an issue. Thank you Smilie.
# 7  
Old 01-04-2017
sed
Code:
sed -E  's/(\w+):([0-9]+)-([0-9]+)\|(.*)/\1\t\2\t\3\t\1:\2-\3\t.\t\4/' file

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