updateDocs

docs/source/api.rst

@@ -1,29 +1,35 @@
 ======================================================
-pyrpipe: python RNA-Seq pipelines
+pyrpipe
 ======================================================
 
-Introduction
-============
+Specifying RNA-Seq data
+=======================
 
-Pysam is a python module that makes it easy to read and manipulate
-mapped short read sequence data stored in SAM/BAM files.  It is a
-lightweight wrapper of the htslib_ C-API.
+Use the :py:mod:`sra` module to create an :class:`SRA` object::
 
-This page provides a quick introduction in using pysam followed by the
-API. See :ref:`usage` for more detailed usage instructions.
+	from pyrpipe import sra
+	sra_obj = sra.SRA(srr_accession="SRR976159")
 
-To use the module to read a file in BAM format, create a
-:class:`~pysam.AlignmentFile` object::
+After the object is created, download the raw data to disk using the 
+:meth:`SRA.download_sra` method::
+	sra_obj.download_sra()
+This will download the raw data in .sra format.
+To convert .sra file to fastq, use :meth:`SRA.run_fasterqdump` method::
 
-   import pysam
-   samfile = pysam.AlignmentFile("ex1.bam", "rb")
+	sra_obj.run_fasterqdump()
 
-Once a file is opened you can iterate over all of the read mapping to
-a specified region using :meth:`~pysam.AlignmentFile.fetch`.  Each
-iteration returns a :class:`~pysam.AlignedSegment` object which
-represents a single read along with its fields and optional tags::
+The sra_obj will keep track of all the downloaded data. The location of downloaded data could be accesed by::
 
-   for read in samfile.fetch('chr1', 100, 120):
-	print read
+	sra_obj.location
 
-   samfile.close()
+To get the paths to sra of fastq files, use::
+
+	sra_obj.localSRAFilePath
+	sra_obj.localfastqPath
+	#for paired
+	sra_obj.localfastq1Path
+	sra_obj.localfastq1Path
+
+
+Performing read alignment
+=========================

docs/source/index.rst

@@ -8,7 +8,8 @@ pyrpipe: python RNA-Seq pipelines
 *****
 Introduction
 *****
-pyrpipe (Pronounced as "pyre-pipe") is a python package to easily develop RNA-Seq analyses workflow by integrating popular RNA-Seq analysis programs. 
+pyrpipe (Pronounced as "pyre-pipe") is a python package to easily develop RNA-Seq analyses workflow by integrating popular RNA-Seq analysis programs.
+pyrpipe allows coding RNA-Seq workflows in pure python in an object oriented manner. pyrpipe provides a high level API to many popular RNA-Seq tools for easier and faster development.
 pyrpipe can be used on local computers or on HPC environments to manage analysis of RNA-Seq data.
 
 To install the latest release, type::