This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Make transeq add identifier to each line

I recently installed transeq and used ti to create six protein sequences from a fasta file created via de novo assembly. The issue is that all the sequences in the file have the same identifier in from of them. Is there a command to have transeq copy the identifiers from the fasta file for each nucleotide sequences and add them only to the appropriate protein sequences?

protein emboss transeq
• 2,303 views • link
written by onspotproductions onspotproductions

Provided a file in that same manner and am running EMBOSS 6.5.7 as I couldn't find 6.6.

• 0 views • link
written by onspotproductions onspotproductions

Depending on your linux distribution, EMBOSS 6.6.0 may be the version on official repositories. Here is a link to EMBOSS 6.6.0 sources, from Debian.

• 0 views • link
updated by Ram Ram • written by h.mon h.mon

1 answer

My transeq does that by default, which version do you use and how do you call it? I have EMBOSS:6.6.0.0

If you provide a file like this:

>id1
...
>id2
...
>id3
...

Output of transeq -frame=1:

>id1_1

>id2_1

>id3_1
• 0 views • link
updated by Ram Ram • written by Michael Dondrup Michael Dondrup

Log in to answer this question.

More posts like this