Recent changes to Concepts

WikiPage Concepts modified by Martin Lindner

Martin Lindner — Wed, 21 Mar 2012 13:00:08 -0000

--- v3 
+++ v4 
@@ -24,3 +24,10 @@
 * __Similarity Estimation__: Do a `import create_matrix` to gain access to the fuctions for calculating the similarity matrix.
 * __Similarity Correction__: Do a `import correct_abundances` to gain access to the fuctions for estimating the true abundances.
 
+
+Wrapper
+=======
+GASiC strongly relies on external software for __read mapping__ and __read simulation__. Since GASiC should work with any mapping tool supporting the SAM format (http://samtools.sourceforge.net/), the user can decide which tool should be used. 
+
+GASiC already provides wrappers for the mapping tools `bowtie, bowtie2`, and `BWA` and for the read simulators `Mason` and `dwgsim`. More wrappers can be added easily by creating a simple wrapper function and adding this wrapper function to the corresponding wrapper list. Step by step instructions are given in the source code `core/tools.py`.
+

WikiPage Concepts modified by Martin Lindner

Martin Lindner — Wed, 21 Mar 2012 12:34:38 -0000

--- v2 
+++ v3 
@@ -21,6 +21,6 @@
 Instead of running the command line scripts one by one, all steps can be bundled in a single python script file. To this end, the user can import the corresponding modules and access the underlying functions directly.
 
 * __Read mapping__: Wrappers for the read mapping tools are available in `core/tools.py`. Just do a `from core import tools` to get access to all implemented wrappers.
-*__Similarity Estimation__: Do a `import create_matrix` to gain access to the fuctions for calculating the similarity matrix.
-*__Similarity Correction__: Do a `import correct_abundances` to gain access to the fuctions for estimating the true abundances.
+* __Similarity Estimation__: Do a `import create_matrix` to gain access to the fuctions for calculating the similarity matrix.
+* __Similarity Correction__: Do a `import correct_abundances` to gain access to the fuctions for estimating the true abundances.

WikiPage Concepts modified by Martin Lindner

Martin Lindner — Wed, 21 Mar 2012 12:34:08 -0000

--- v1 
+++ v2 
@@ -1,18 +1,26 @@
-GASiC Concepts
+Interfaces
 ==============
 
-There are two major approaches to use GASiC. The first is the _command line interface_, the second is the _scripting interface_.
+There are two major approaches to use GASiC. The first is the __command line interface__, the second is the __scripting interface__.
 
 Command Line Interface
 ----------------------
 
 For the command line interface, GASiC provides three python scripts:
 
 * `run_mappers.py` perfroms read alignment/mapping. The generated output is in a format readily usable by the following GASiC steps.
 * `create_matrix.py` calculates the similarity matrix encoding the sequence similarities of the reference genomes.
 * `correct_abundances.py` estimates the true abundances for all genomes in the dataset using the alignment information and the similarity matrix.
 
 
 Scripting Interface
 -------------------
+
+GASiCs scripting interface allows the user to create more versatile and powerful analysis scripts. This is useful, when tasks should be automated or a finer control of the single steps is required.
+
+Instead of running the command line scripts one by one, all steps can be bundled in a single python script file. To this end, the user can import the corresponding modules and access the underlying functions directly.
+
+* __Read mapping__: Wrappers for the read mapping tools are available in `core/tools.py`. Just do a `from core import tools` to get access to all implemented wrappers.
+*__Similarity Estimation__: Do a `import create_matrix` to gain access to the fuctions for calculating the similarity matrix.
+*__Similarity Correction__: Do a `import correct_abundances` to gain access to the fuctions for estimating the true abundances.

WikiPage Concepts modified by Martin Lindner

Martin Lindner — Wed, 21 Mar 2012 10:02:30 -0000

GASiC Concepts ============== There are two major approaches to use GASiC. The first is the _command line interface_, the second is the _scripting interface_. Command Line Interface ---------------------- For the command line interface, GASiC provides three python scripts: * `run_mappers.py` perfroms read alignment/mapping. The generated output is in a format readily usable by the following GASiC steps. * `create_matrix.py` calculates the similarity matrix encoding the sequence similarities of the reference genomes. * `correct_abundances.py` estimates the true abundances for all genomes in the dataset using the alignment information and the similarity matrix. Scripting Interface -------------------