src/spartan/utils/annotations/ensembl/gff3.py:
- added load_genes_gffutils(gff3_path)
 On branch feat/get_upstream
 Changes to be committed:
	modified:   setup.py
	modified:   src/spartan/utils/annotations/ensembl/gff3.py
	new file:   src/spartan/utils/dev/__init__.py
	renamed:    src/spartan/utils/annotations/ensembl/gff3.py -> src/spartan/utils/annotations/gffutils.py
	new file:   testing/gff3/test1.ensembl.gff3
	new file:   testing/gff3/test1.ensembl.gff3.db
	new file:   testing/gff3/test1.ensembl.gff3.db-shm
	new file:   testing/gff3/test1.ensembl.gff3.db-wal
src/spartan/utils/annotations/gffutils.py:
- renamed load_genes() to load_gff3()
renamed:    src/spartan/utils/annotations/gffutils.py -> src/spartan/utils/annotations/gffutils_helpers.py
created fastas.py and moved fasta related classes/functions to there
fixed a bit of the fastas.py documentations
created files:
- utils/annotations/ensembl/gff3.py
- utils/annotations/intervals.py
src/spartan/utils/annotations/intervals.py:
- added class CompoundFeature
- added class SimpleFeature
- docstring outlined SimpleFeature
src/spartan/utils/annotations/ensembl/gff3.py
- added SimpleFeatureGFF3(intervals.SimpleFeature)
added todos  to both and an overlap detector to intervals
src/spartan/utils/annotations/intervals.py:
- added def left_window_coords(win_size, original_left_bound)
- added def right_window_coords(win_size, original_right_bound):
src/spartan/utils/annotations/ensembl/gff3.py
src/spartan/utils/annotations/ensembl/gff3.py:
- added class GFF3/__init__/install_gff3_features_from_file
- modified class SimpleFeatureGFF3:
	* added SUPER __init__ call
	* commented @staticmethod for parse_attributes because of call sig issues
	* renamed self.data.attributes.unnamed to 'unnamed_attributes'
	* added def get_range()
	* def get_upstream and def get_downstream now alter data.source and data.type
	* added def get_parent_ID and def set_parent_ID
src/spartan/utils/annotations/intervals.py:
- class SimpleFeature:
	* added self.data to match data in inherited models
/home/gus/Dropbox/repos/git/spartan/src/spartan/utils/annotations/ensembl/gff3.py:

- def parse_gff3(gff3_path):
	* added 'save line number to feature
- class GFF3(object):
	* added feature.uniq_id creation
	* added translation dicts between uniq_id and common ID
	* self.parent_graph uses feature.Uniq_id as nodes
added /home/gus/Dropbox/repos/git/spartan/testing/fasta/AGAP004685.fasta*
/home/gus/Dropbox/repos/git/spartan/src/spartan/utils/annotations/ensembl/gff3.py:

- class GFF3(object):
	* added fasta access through pyfasta
src/spartan/utils/annotations/intervals.py:

- class SimpleFeature(object):
	* def __cmp__(self, other): wrote it
	* def __eq__(self, other): wrote it
Merge branch 'feat/get_upstream' into dev
src/spartan/utils/annotations/intervals.py:
- finished operator overloading