<commit_before>.. pyGeno documentation master file, created by
   sphinx-quickstart on Thu Nov  6 16:45:34 2014.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

pyGeno: Ensembl, Next-Gen Sequencing, dbSNP together on your laptop
===================================================================

pyGeno's `lair is on Github`_.

.. _lair is on Github: http://www.github.com/tariqdaouda/pyGeno

A Quick Example:
-----------------
pyGeno is a personal bioinformatic database that runs directly into python and on your laptop. 
pyGeno is here to make extracting data such as gene sequences a breeze.

.. code::

	from pyGeno.Genome import *

	g = Genome(name = "GRCh37.75")
	prot = g.get(Protein, id = 'ENSP00000438917')[0]
	#print the protein sequence
	print prot.sequence
	#print the protein's gene biotype
	print prot.gene.biotype
	#print protein's transcript sequence
	print protein.transcript.sequence

	...

	#fancy queries
	for exons in g.get(Exons, {"CDS_start >": x1, "CDS_end <=" : x2, "chromosome.number" : "22"}) :
		#print the exon's coding sequence
		print exon.CDS
		#print the exon's transcript sequence
		print exon.transcript.sequence

	...

	#and you can do the same for your subject specific genomes
	g = Genome(name = "GRCh37.75", SNPs = ["STY21_RNA"], SNPFilter = MyFilter())


Verbose Introduction
---------------------

pyGeno integrates:

* **Reference sequences** and annotations from **Ensembl**<commit_msg>Update index.rst<commit_after>.. pyGeno documentation master file, created by
   sphinx-quickstart on Thu Nov  6 16:45:34 2014.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

pyGeno: Ensembl, Next-Gen Sequencing, dbSNP together on your laptop
===================================================================

pyGeno's `lair is on Github`_.

.. _lair is on Github: http://www.github.com/tariqdaouda/pyGeno

A Quick Example:
-----------------
pyGeno is a personal bioinformatic database that runs directly into python and on your laptop. 
pyGeno is here to make extracting data such as gene sequences a breeze.

.. code::

	from pyGeno.Genome import *

	g = Genome(name = "GRCh37.75")
	prot = g.get(Protein, id = 'ENSP00000438917')[0]
	#print the protein sequence
	print prot.sequence
	#print the protein's gene biotype
	print prot.gene.biotype
	#print protein's transcript sequence
	print protein.transcript.sequence

	...

	#fancy queries
	for exons in g.get(Exons, {"CDS_start >": x1, "CDS_end <=" : x2, "chromosome.number" : "22"}) :
		#print the exon's coding sequence
		print exon.CDS
		#print the exon's transcript sequence
		print exon.transcript.sequence

	...
	#You can do the same for your subject specific genomes
	#by combining a reference genome with polymorphisms 
	g = Genome(name = "GRCh37.75", SNPs = ["STY21_RNA"], SNPFilter = MyFilter())

Verbose Introduction
---------------------

pyGeno integrates:

* **Reference sequences** and annotations from **Ensembl**
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