1 answer
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.
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written
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Travis Wheeler
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
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written
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Travis Wheeler
Notably you actually need to use --domtblout domains.txt because --tblout hits.txt doesn't give you per-alignment fields such as the position.
If you do --domtblout, you get a table with this header (and therefore these fields):
# --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord
# target name accession tlen query name accession qlen E-value score bias # of c-Evalue i-Evalue score bias from to from to from to acc description of target
#------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
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