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Question: Set a %coverage threshold during a hmmsearch using HMMer
0
gravatar for CrLs
6.2 years ago by
CrLs • 10
France
CrLs • 10 wrote:

Hi everyone,

I would like to know if there is a way to set a %coverage treshold using hmmsearch. I've read the user guide, but i haven't found it.

 

Regards,

C.
sequence • 2.0k views
ADD COMMENT • link •
modified 6.2 years ago by Travis Wheeler • 100 • written 6.2 years ago by CrLs • 10
1
gravatar for Travis Wheeler
6.2 years ago by
Travis Wheeler • 100
United States
Travis Wheeler • 100 wrote:

You'll need to provide a definition of "%coverage" to be sure, but the answer is almost certainly "no". 

When I hear "%coverage", I think of a measure of shared length, probably "what percent of the sequence is aligned to the model" (or vice versa).  If this is what you're after, you may want to use hmmsearch's --tblout flag. This will give you an easy-to-parse space-delimited file that includes start/end-positions for both the query model and the target sequence, along with the total target sequence length. Knowing the model length also, the %coverage math from there is pretty easy to pull off.
ADD COMMENT • link written 6.2 years ago by Travis Wheeler • 100

Hello Travis,

That's a great answer. Have you any advice on which parser i should use ? If there is one for python or perl ?

Thaks again !

ADD REPLY • link written 6.2 years ago by CrLs • 10
1

I recommend writing your own "parser".  First run hmmsearch

% hmmsearch --tblout my_output.tblout  query.hmm  target.fa

Then look at the format of the file produced when using hmmsearch's --tblout flag  (in the example above: my_output.tblout). You'll find that this is likely the easiest parsing task you'll ever do.  Simply walk through the lines of the table file one-at-a-time, (a) ignoring lines starting with "#", and (b) accessing the content of each line using either split or a regex (I'm imagining Perl here).   Heck, you could even use awk to parse the file, if you're a fan of awk

 

ADD REPLY • link written 6.2 years ago by Travis Wheeler • 100

Ok. Thanks for you time and your answer. i'll try. (i'd give you a 'biostar gold' if it was available)

ADD REPLY • link written 6.2 years ago by CrLs • 10
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