Make alignment flexible

naturalis / supersmart

Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa

MIT License

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Make alignment flexible #4

Closed rvosa closed 10 years ago

rvosa commented 10 years ago

We need to provide users with the option to specify which alignment tool to use, both for cluster alignment and profile alignment. It is probably best to do this by setting both separately in phylota.ini, and then having AlignmentService subclasses (::muscle, ::mafft, etc.) which are loaded by the SequenceGetter.

rvosa commented 10 years ago

Here's probably how we might do this:

in phylota.ini the user specifies which aligner to use: T-Coffee, Muscle, MAFFT, Clustal, etc.
from that name, we map onto one of the subclasses of Bio::Tools::Run::Alignment
we dispatch as we now only do for muscle, unfortunately no aligner-specific parameters as yet

rvosa commented 10 years ago

As of revision c6732b84b6f2cf6dd775256a655e6d444e4ee6bc, the SequenceGetter can wrap around very many different alignment tools, namely: mafft, clustalw, kalign, muscle, probalign, probcons, tcoffee, and amap. The user preference for which one to use is specified in phylota.ini (key: MSA_TOOL). The unit test t/align.t verifies this behaviour.

rvosa commented 10 years ago

As of revision a530bd06ef44934624562fb4eb47fc0bb44ac0ac, the puppet manifest includes the steps for installing MAFFT, which is the other preferred aligner (next to muscle) that we want to install by default.