headers from multifasta files
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3.6 years ago

I have a folder with multifasta files and I would like to extract the headers from each one of them, I've used the following command in shell

 grep -e ">" *.fasta > prueba_nc.txt

the output looks like it

Adenoviridae_genomas.fasta:>AC_000001 [AC_000001] Ovine adenovirus A, complete genome.
Adenoviridae_genomas.fasta:>AC_000002 [AC_000002] Bovine adenovirus B, complete genome.
Adenoviridae_genomas.fasta:>AC_000003 [AC_000003] Canine adenovirus 1, complete genome.

...

and I would like to extract only the fragment after the ">"

sequence • 1.7k views
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I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

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Did you upvote just my answer? Please validate the other answers and provide feedback, if at all possible. Muchas gracias.

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You are absolutely right Kevin, I have upvoted it ;-)

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Okay, thanks. Did you look at the other solutions by the others?

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Hi Ulises, although this can be easily achieved as other people has already explained, if you are working with FASTA files you may be interested in SEDA (http://www.sing-group.org/seda/). Please, take a look and feel free to contact us if you need some assistance using it. Regards.

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3.6 years ago

Prueba del éxito:

cat and cut

cat prueba_nc.txt | cut -f2 -d'>'
AC_000001 [AC_000001] Ovine adenovirus A, complete genome.
AC_000002 [AC_000002] Bovine adenovirus B, complete genome.
AC_000003 [AC_000003] Canine adenovirus 1, complete genome.

cut

   cut -f2 -d'>' prueba_nc.txt
   AC_000001 [AC_000001] Ovine adenovirus A, complete genome.
   AC_000002 [AC_000002] Bovine adenovirus B, complete genome.
   AC_000003 [AC_000003] Canine adenovirus 1, complete genome.

AWK

awk '{print $2}' FS=">" prueba_nc.txt
AC_000001 [AC_000001] Ovine adenovirus A, complete genome.
AC_000002 [AC_000002] Bovine adenovirus B, complete genome.
AC_000003 [AC_000003] Canine adenovirus 1, complete genome.
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3.6 years ago

So you want to get rid of the filename?

In that case, use the -h/--no-filename option of grep.

Or you also want to get rid of the >? You could pipe the grep to sed, e.g.:

grep -he ">" *.fasta | sed 's/^>//' > prueba_nc.txt
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$ sed -n '/>/ s/>//p' *.fa

also works.

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3.6 years ago
st.ph.n ★ 2.6k
for file in *.fasta; do grep -e '>' | cut -f 2 -d '>' > "`basename .fasta`.headers.txt"; done

Will take each file with .fasta extension in your cwd and grep for the headers, and cut the headers and take everything after the '>' and place them into a file named with the prefix from the original fasta file now with the extension .headers.txt

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3.6 years ago

Using seqkit

seqkit fx2tab -in *.fa > headers.txt
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$ seqkit seq -n test.fa

also works

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