Blast results processing lines bigger than 60
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3 months ago
hdtms ▴ 20

Hi,

I have a doubt processing blast results in linux command line with a column I added, I want the cov result to be bigger than 60. But I can't make this command work. All works except {cov > 60} I also tried (cov > 60) but it doesn't select the results bigger than 60. I must also say that I started by thinking that the cov result would be in decimal like 0.63 but I noticed it gives results in 63.xxx.

Any suggestion would be greatly appreciated.

for file in *.join; do echo $file ; awk '{cov = $4/$13}{cov > 60}{print $1, $2, $3}' $file >> ../MUSTARD_NEW_RESULTS_FILTERED/$file.filtered; done
blast unix commands awk result • 306 views
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What format is your blast output in?

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Output format 6

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I also rechecked the command and it turns out that the only part that is working is the print command.

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