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Trim the ID line of a fasta

I have a fasta file with some very silly ID's (straight from NCBI) that look like this: 

>KF859747.1 HIV-1 isolate DEURF09UG005 from Uganda gag protein (gag) gene, complete cds; pol protein (pol) gene, partial cds; vif protein (vif), vpr protein (vpr), tat protein (tat), rev protein (rev), vpu protein (vpu), and envelope glycoprotein (env) genes, complete cds; and nonfunctional nef protein (nef) gene, complete sequence

If all I wanted was the >KF859747 part to be in my fasta, are there any nifty one liners to do this on the command line?

fasta regex
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updated by lieven.sterck lieven.sterck • written by SaltedPork SaltedPork

In case you are interested in obtaining such headers using a desktop GUI application, you may have a look at our SEDA software (http://www.sing-group.org/seda/). It has different options for processing headers as well as obtaining them using the "Statistics" option. Regards.

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written by Hugo Hugo

Hello SaltedPork!

Commonly asked question. Please search Biostars first in future.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by GenoMax GenoMax

2 answers

Something like 

cat blabla.fasta | cut -f 1 -d " " > output.fasta

That should keep your FastA sequence, as it simply returns the first column (-f 1) of each row before a single dash (-d " ") .

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written by apeltzer apeltzer

same principle but with sed

cat file.fasta | sed 's/ .*//g' > out.fasta
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written by lieven.sterck lieven.sterck

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