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SpliceV
===================================
.. toctree::
   :maxdepth: 2
   :caption: Contents:


Installation
____________

Install via pip:

``pip install SpliceV``

Download source code:

``git clone https://github.com/flemingtonlab/SpliceV``

Dependencies
____________

* pysam
* matplotlib
* numpy

Tutorial
_________

The minimal requirements for running SpliceV are:

1) BAM file

2) GTF file
   
The program will sort and/or index BAM files if this wasn't done.

The simplest way to plot, using the gene OAS2:

``$ SpliceV -b sample1.bam -gtf gencode.v29.basic.annotation.gtf -g OAS2``

.. image::  /_static/example1.jpg

To *filter* out low abundance junctions, use the ``-f`` flag:

``$ SpliceV -b sample1.bam -gtf gencode.v29.basic.annotation.gtf -g OAS2 -f 5``

.. image:: /_static/example2.jpg

Change the *color* using the ``-c`` flag (can specify hex "#2a9c3c" or RGB or simply, "green").

``$ SpliceV -b sample1.bam -gtf gencode.v29.basic.annotation.gtf -g OAS2 -f 5 -c \#2a9c3c``

.. image:: /_static/example3.jpg

*Plot predicted binding sites* for an RNA binding protein (in this case, HNRNPK) with ``-rnabp``. This requires a genome fasta file specified by ``-fa``. 

``$ SpliceV -b sample1.bam -gtf gencode.v29.basic.annotation.gtf -g OAS2 -f 5 -c \#2a9c3c -rnabp HNRNPK -fa hg38.fa``

.. image:: /_static/example4.jpg

To *plot back-splice junctions*, if the aligner used outputs chimeric alignments using the 'SA' tag (such as STAR v2.5+ using the --chimSegmentMin and --chimOutType WithinBAM), only the bam file is required. Otherwise, use the ``-bsj`` flag to point to a file containing junction coordinates and counts (formats described below).

``$ SpliceV -b polya.bam rnaseA.bam -gtf gencode.v29.basic.annotation.gtf -g CEP128 -f 5``

.. image:: /_static/example5.jpg

*Normalize exon-level expression between samples* with the ``-n`` flag

``$ SpliceV -b sample1_polya.bam sample1_rnaseA.bam -gtf gencode.v29.basic.annotation.gtf -g CEP128 -f 5 -n``

.. image:: /_static/example6.jpg

Input file formats
__________________

Splice junction (``-sj``) and back-splice junction (``-bsj``) calls should be *tab-separated* input files with each line representing the coordinates of one junction in this order: chromosome, smaller coordinate, larger coordinate, strand, counts. Files should contain no header line.

For example: 

.. code-block::  none

        chr1    123     1234    +       55
        chr2    342     53545   -       4
        chr2    1000    1200    -       909



Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`