Implement taxid-based blastn (#147)

sdhutchins commented 5 years ago

Changes

Improved BaseFTPClient API (exposed a user and password, deprecated email).
Migrated BaseBlastN and OrthoBlastN to blast.py
Renamed top-level folders 😨 except the package/module name (OrthoEvol) to lowercase to fit with Python packaging standards

Added downloading of /blast/db/v5/ NCBI databases that include taxonomy identification.
Created an OrthoBlastN class for hardcoded and standardized blastn parameters and methods. It is built on top of the BaseBlastN method which has been improved to expose more of the Comparative Genetics API.
Implemented color for CRITICAL logging level.
Added verbose parameter to BaseBlastN
Added the ability to use an existing directory for project_path in standalone_config function.

Addresses #143

grabear commented 5 years ago

Still WIP? @sdhutchins

sdhutchins commented 5 years ago

Still WIP? @sdhutchins

Now that the lab is more or less set up minus a little more organizing and some labeling...I will focus on this tomorrow. Not much left to do here.

grabear commented 5 years ago

@sdhutchins Nice! I'm going to start on the SGE rework today.

sdhutchins commented 5 years ago

With proj_mana set to None, the test for BaseBlastN is passing.

See more about this in #149. If you have thoughts on it, let me know. @grabear

sdhutchins commented 5 years ago

@grabear It's ready for review (finally...). Take your time.

grabear commented 5 years ago

@sdhutchins Reviewing now.

sdhutchins commented 5 years ago

I added a ref_species parameter. Let me know what you think. Should be satisfactory now.