Question: Make transeq add identifier to each line
0
gravatar for onspotproductions
3.5 years ago by
United States
onspotproductions130 wrote:

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?

transeq emboss protein • 874 views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by onspotproductions130
0
gravatar for Michael Dondrup
3.5 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

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
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Michael Dondrup46k
0
gravatar for onspotproductions
3.5 years ago by
United States
onspotproductions130 wrote:

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

ADD COMMENTlink written 3.5 years ago by onspotproductions130

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.

ADD REPLYlink written 3.5 years ago by h.mon26k
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