Environment and directory structure updates

[evanroyrees]

This is partially to display the git workflow via forks, pull requests, reviews and merges. You do not need to do a comprehensive review here. These edits are minor and should work out some of the kinks I have encountered while testing on the Boreal datasets as well as on my Mac

Updates

• Removed unused scripts
• Changed shebang where env now specifies python instead of python3 (This otherwise results in a cryptic error. Thank you, @cfrancoeur for bringing this to my attention.
• Added ncbi directory under databases using .gitignore. (This will ensure the user has the required database directories when downloading NCBI or markers files, respectively)
• Post-processing scripts are in a validation directory
• Updated parameters in tests/metagenome.config
• Minor tqdm edit in lca.py to display thousand delimiter for ORFs search description.
• Added bhsne.py under binning directory to provide user capability to run python2.7 BH-tSNE (Note: conda env setup is within bhsne.py script.
• Bug fix to hmmer.py main script where input and output args were the same. Updated argparse parameters accordingly.
• Suppressed numba logger at DEBUG level in kmers.py
• Updated kmers.py args with default --n-components=2 and --do-pca as well as --pca-dimensions are now available in the main call to kmers.
• Minor edits to README.md with information on the first version of Autometa and how to construct a coverage table with the current iteration (in dev)
• Created a datasets directory to which will be populated with functions to easily retrieve data specified in upcoming Autometa releases. I.e.

Example usage of scripts populating datasets directory

from autometa.datasets import simulated_community
from autometa.datasets import synthetic_community
# Retrieve specified simulated community
fasta = simulated_community.get('78.125')
# Retrieve all simulated communities mentioned.
fastas = simulated_community.get('all')
# Same for synthetic, etc...
fasta = synthetic_community.get('MIX51')

[jason-c-kwan]

I'm going to have to finish my review of the refactored code first before I can assess this. Is that OK? I just would feel better understanding the code first.

[evanroyrees]

Yes, no problem. Since I have a fork of the repository, I can operate on my own repo until the changes are merged.