updateDocs

docs/source/api.rst

@@ -1,35 +1,36 @@
-======================================================
-pyrpipe
-======================================================
+************
+pyrpipe API
+************
 
-Specifying RNA-Seq data
+sra
 =======================
 
-Use the :py:mod:`sra` module to create an :class:`SRA` object::
+The :py:mod:`sra` module contains the SRA class.
 
-	from pyrpipe import sra
-	sra_obj = sra.SRA(srr_accession="SRR976159")
 
-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::
+SRA
+^^^^
+The :class:`SRA` class encapsulates RNA-Seq data.
 
-	sra_obj.run_fasterqdump()
 
-The sra_obj will keep track of all the downloaded data. The location of downloaded data could be accesed by::
+assembly
+=========
+The :py:mod:`assembly` module contains classes for transcript assembly tools.
 
-	sra_obj.location
+mapping
+=========
+The :py:mod:`mapping` module contains classes for read alignment.
 
-To get the paths to sra of fastq files, use::
 
-	sra_obj.localSRAFilePath
-	sra_obj.localfastqPath
-	#for paired
-	sra_obj.localfastq1Path
-	sra_obj.localfastq1Path
+quant
+=========
+The :py:mod:`quant` module contains classes for transcript quantification tools.
 
+qc
+=========
+The :py:mod:`qc` module contains classes for fastq quality control tools.
 
-Performing read alignment
-=========================
+
+tools
+=========
+The :py:mod:`tools` module contains classes for various RNA-Seq tools.

docs/source/index.rst

@@ -5,9 +5,9 @@ pyrpipe: python RNA-Seq pipelines
 :Date: |today|
 :Version: |version|
 
-*****
+*************
 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 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.
@@ -26,8 +26,8 @@ Contents
 .. toctree::
    :maxdepth: 2
 
-   api.rst
    usage.rst
+   api.rst
    installation.rst
    faq.rst
    developer.rst

docs/source/usage.rst

@@ -0,0 +1,40 @@
+======================================================
+Basic usage
+======================================================
+
+Specifying RNA-Seq data
+=======================
+
+Use the :py:mod:`sra` module to create an :class:`SRA` object::
+
+	from pyrpipe import sra
+	sra_obj = sra.SRA(srr_accession="SRR976159")
+
+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::
+
+	sra_obj.run_fasterqdump()
+
+The sra_obj will keep track of all the downloaded data. The location of downloaded data could be accesed by::
+
+	sra_obj.location
+
+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
+=========================
+The :py:mod:`mapping` module contains several classes to access read alignment tools.
+The method :meth:`perform_alignment` can be used with the SRA object.
+An example using Hisat2::
+	hs=mapping.Hisat2(hisat2_index="",**hsOpts)
+	hs.perform_alignment(ob,**{"-p":"10"})