Renaming Entry In Fasta File
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3.9 years ago
stan.aanhane ▴ 30

I want to change my entries in my fasta file, but I want to keep certain numbers. I work with Linux

For example

Current names:

>NODE_1_length_140009_cov_0.223002

>NODE_2_length_119367_cov_0.245541

>NODE_3_length_108076_cov_0.169347

And I want them to change to:

>lclav_contig 1 lengte 140009 cov 0.223002

>lclav_contig 2 lengte 119367 cov 0.245541

>lclav_contig 3 lengte 108076 cov 0.169347

I know i have to work with awk but I'm stuck at the moment. Thank you for the help in advance!

Fasta Linux • 713 views
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You can use sed to make two changes. Replace _ with space and then NODE with lclav_contig. I assume lengte is an error but if not that will be the third replacement.

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Thank you!

lengte is length in my native langue so no error ;)

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3.9 years ago
Biogeek ▴ 470

sed 's/NODE/lclav_contig/' {INPUT FILE} | sed 's/_/ /g' | sed 's/ /_/1' > {OUTPUT FILE}

*Apologies, should have replied inline.

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Thank you! This worked fine!

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3.9 years ago
echo '>NODE_1_length_140009_cov_0.223002' | sed -re 's/>[A-Z]+_([0-9])_[a-z]+_([0-9]+)_([a-z]+)_(.*)/>lclav_contig \1 lengte \2 \3 \4/g'

>lclav_contig 1 lengte 140009 cov 0.223002

Most of the tools stop handling characters after first space. New headers (new format) may create a problem, in future.

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