added default moltype for infernal

[gregcaporaso]

this should have been part of #19

[gregcaporaso]

Be sure to view this one with whitespace hidden when reviewing (this link will show you the diff with whitespace hidden).

[gregcaporaso]

@josenavas, can you review this one? Need it for a QIIME PR.

[squirrelo]

Just out of curiosity, why DNA as default instead of RNA when the tool is built with RNA in mind?

[josenavas]

The code looks good. As we now there is no way of testing this before merging, so we can merge, run it through QIIME and check that it didn't broke anything.

@gregcaporaso once you provide an answer to @squirrelo I'll merge this

[gregcaporaso]

@squirrelo, it's because the only place that we're using brokit is QIIME, where we're passing DNA sequences in. (This whole package is kind of a necessary evil to remove the PyCogent dependency from QIIME.)

[gregcaporaso]

Note that I tested locally and the change works.

[squirrelo]

Fair enough. This is just something that's going to come up when brokit is
phased out for whatever is next, so figured it would be good to bring up
now.

On Tue, May 13, 2014 at 10:43 PM, Greg Caporaso [email protected]:

@squirrelo https://github.com/squirrelo, it's because the only place
that we're using brokit is QIIME, where we're passing DNA sequences in.
(This whole package is kind of a necessary evil to remove the PyCogent
dependency from QIIME.)

—
Reply to this email directly or view it on GitHubhttps://github.com//pull/23#issuecomment-43041644
.

[josenavas]

Thanks @gregcaporaso merging.

@squirrelo this repo should be used only on QIIME until we decide which app controllers do we actually want to include in skbio. Then, they'll be recoded....

[gregcaporaso]

Thanks!