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#1
03-03-2012
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Awk pattern with letters and forward slash
Hi, I have a tab delimited file "test.txt" like this: Code:
id1 342 C/T id2 7453 T/A/-/G/C id3 531 T/C id4 756 A/T/G id5 23 A/G id6 717 T/A/C id7 718 C/T/A And so on, with the possible choices for letters being A,C,T,G. I would like to exclude from my file all the lines that do not have exactly any of the letters split by forward slash, followed by any of the letters. So I would like my file to look like this: Code:
id1 342 C/T id3 531 T/C id5 23 A/G I have not been able to find a good regex for this. I have tried: Code:
awk '{ if($3 !='/([ACTG]\)/([ACTG]/)' {print}}' test.txtBut it does not work, can you please tell me what I am doing wrong? Thank you for your help. -francy Last edited by Scott; 03-03-2012 at 08:18 AM.. Reason: Please use code tags |
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#2
03-03-2012
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Code:
$ awk '$3 ~ /^[ACTG]\/[ACTG]$/' file id1 342 C/T id3 531 T/C id5 23 A/G |
| The Following User Says Thank You to Scott For This Useful Post: | ||
francy.casa (03-03-2012) | ||
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#3
03-03-2012
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Thank you very much Scott! I was making it more complicated with useless curly brackets. Thanks!
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#4
03-03-2012
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You were close. The real difference is in using the match operator (~) instead of the equals operator (=).
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francy.casa (03-03-2012) | ||
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