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Substitute first column based on second column

Hi,

I have files with lines that look like

HSQ1008:141:D0CC8ACXX:3:1106:17255:124378       163     chr14

I'm wondering how I can output a file that appends /1 if the second column is 99 or 83 and a /2 if the second column is 163 or 147. Also I want to put \n + \n between each the second and third column, a \n after the first and last column, and an "@" in front of the very first column. So I would want the above line to become

@HSQ1008:141:D0CC8ACXX:3:1106:17255:124378/2
163
+
chr14

I appreciate any help!

awk
• 2,415 views • link
updated by Ram Ram • written by jyu429 jyu429

1 answer 

awk '{if ($2 == 99 || $2 == 83) print "@",$1,"/1\n",$2,"\n+\n",$3"\n"; else if ($2 == 163 || $2 == 147) print "@",$1,"/2\n",$2,"\n+\n",$3,"\n"; else {}}'  sam_file.sam

I haven't tested it but you should tweak around and make it to work if it throws any error.

• 0 views • link
updated by Ram Ram • written by Ashutosh Pandey Ashutosh Pandey

Thanks! Just needed to take the commas out but this worked great!

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written by jyu429 jyu429

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