Trails - Add biopython functions

[maxbates]

Need to wrap additional functions for Clotho Intro trail

• revcomp
• ligate
• PCR
• digest

others?

[maxbates]

@billcao @KelvinLi I know you guys are busy with finals, and this can wait a week, but I'd like to get the functions we need for the Intro Trail in soon (by the 20th or so)... This will require wrapping some of bioPython, and whatever functions Bill wrote. Each function for this release will need to be wrapped as its own clotho function, and argument types noted.

[KelvinLi]

Yup, and we'll need the run refactor to be done too.

Thanks, Kelvin

On Mon, 2014-05-12 at 18:37 -0700, Maxwell Bates wrote:

@billcao @KelvinLi I know you guys are busy with finals, and this can wait a week, but I'd like to get the functions we need for the Intro Trail in soon (by the 20th or so)... This will require wrapping some of bioPython, and whatever functions Bill wrote. Each function for this release will need to be wrapped as its own clotho function, and argument types noted.

— Reply to this email directly or view it on GitHub.

[maxbates]

@KelvinLi once run refactor is in, how hard will it be to incorporate a set of biopython functions - want to support construction files, so this requires restriction digests, gel purification, ligation, PCR, and some enzymes

[KelvinLi]

First of all, biopython doesn't really do simulations/predictions of PCR, ligation, gels, etc. Good news is PCR prediction has already been implemented by Bill's code (see wiki).

Bad news is I'm kinda out of time to work on Clotho. I'm not going to be involved this summer. I'm spending my last couple of hours cleaning up some run internals.

On Wed, 2014-05-21 at 22:31 -0700, Maxwell Bates wrote:

@KelvinLi once run refactor is in, how hard will it be to incorporate a set of biopython functions - want to support construction files, so this requires restriction digests, gel purification, ligation, PCR, and some enzymes

— Reply to this email directly or view it on GitHub.

[billcao]

Based off of my understanding (please correct me if I'm wrong), incorporating new (Bio)python functions into Clotho involves two parts:

1. Add the respective python file into the directory clotho3/src/main/python/lib/
2. To dispatch the function and make it callable from Clotho, a .json file of the form py_(function name called from Clotho) and correctly populated must be added to the directory clotho3/src/test/resources/testData/

This is based off of what Kelvin sent me previously, and I believe is all we need to know in order to implement further functions that are callable from Clotho.

[KelvinLi]

Almost. All that is strictly needed is the JSON file. But since JSON strings aren't the best place to put complex python code, it is sometimes nice to put the body of the logic into a separate file in src/main/python/lib.

On Wed, 2014-05-21 at 22:56 -0700, Bill Cao wrote:

Based off of my understanding (please correct me if I'm wrong), incorporating new (Bio)python functions into Clotho involves two parts:

1. Add the respective python file into the directory clotho3/src/main/python/lib/
2. To dispatch the function and make it callable from Clotho, a .json file of the form py_(function name called from Clotho) and correctly populated must be added to the directory clotho3/src/test/resources/testData/

This is based off of what Kelvin sent me previously, and I believe is all we need to know in order to implement further functions that are callable from Clotho.

— Reply to this email directly or view it on GitHub.

[maxbates]

doesn't seem like biopython does anything we need for this level of stuff, so closing