[Seqan-dev] Creating a Dependent StringSet

[Hendrik Weisser <hw5@sanger.ac.uk>]

Hi!

I'm working on some code in OpenMS that matches peptides to a protein 
sequence database using SeqAn algorithms. There are two cases:
1. An exact string search of the whole peptide/protein sets, followed by 
an approximate search of only unmatched peptides against only proteins 
with sequence ambiguities.
2. An approximate string search of the whole peptide/protein sets.

I'm starting out with StringSets that store the peptides and proteins, 
which are used in the exact search. For the approximate search, I then 
use Dependent StringSets that I fill with either a subset of the 
peptides/proteins (case 1) or with the whole sets (case 2).

My problem is that in case 2, initializing the Dependent StringSet for 
the proteins is agonizingly slow. For a big protein database with 
>300,000 entries it takes more than a day! It is much, much slower than 
generating the Owner StringSet in the first place.

This is the code I use:

> seqan::StringSet<seqan::Peptide> prot_DB; // full protein DB
> [...]
> seqan::StringSet<seqan::Peptide, seqan::Dependent<seqan::Generous> > prot_DB_SA;  // for approx. search
> Size length_prot_DB = length(prot_DB);
> reserve(prot_DB_SA, length_prot_DB);
> for (Size i = 0; i < length_prot_DB; ++i)
> {
>   assignValueById(prot_DB_SA, prot_DB, i);
> }

Is this just not a good way of doing it?

Based on the documentation of "assignValueById" for StringSets 
(http://docs.seqan.de/seqan/master/class_StringSet.html#StringSet%23assignValueById 
- note that the function is erroneously called "getValueById") I would 
have expected that "assignValueById(prot_DB_SA, prot_DB)" would append 
the whole StringSet, but that doesn't compile.

This is all based on SeqAn 1.4, which OpenMS still uses. Has this 
problem been solved already in the newer releases?


Cheers

Hendrik


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