#cri5t1na

[pacm3n-blog1]

PLINK to the rescue(?)

LiftOver is a necesary step to bring all genetical analysis to the same reference build. LiftOver can have three use cases:

(1) Convert genome position from one genome assembly to another genome assembly

In most scenarios, we have known genome positions in NCBI build 36 (UCSC hg 18) and hope to lift them over to NCBI build 37 (UCSC hg19).

(2) Convert dbSNP rs number from one build to another

(3) Convert both genome position and dbSNP rs number over different versions

It is likely to see such type of data in Merlin/PLINK format.

We will explain the work flow for the above three cases. In the rest of this article, our example is to lift over from lower/older build to newer/higher build, as it is the common practice.

Using different tools, liftOver can be easy. For example, UCSC liftOver tool is able to lift BED format file between builds. With our customized scripts, we can also lift rsNumber and Merlin/PLINK data files.

[pacm3n-blog1]

BUT WHY:

Reasons[0]: Use classes in project; probably appreciated

(not so) Subtly highlight your selfless spirit :p - Sharable

Safe documentation, functionality for future self-use:  submit in repo final clean version, import anytime you re-need

Open Source as a chance to receive feedback for Optimization, tweaking 4 fine-tuning

+++

+++++ [..]

.......................................

[P.S.: Kudos Nats -- > ιδέα για repo-κατάσταση!]

*Note: 

Java-ish rationale for JUST 1 public class per file, can be somehow implemented as a concept in Python as well (duh!), as classes packages organised in seperate files.

TO BE GOOGLED:

empty  __init__.py file

multi file packages Vs one big module

all modules in one folder, appended this path to os.path

http://pydoit.org/ -- The Story:  https://schettino72.wordpress.com/2008/04/14/doit-a-build-tool-tale/

MORE READS:

1. How to organize multiple python files into a single module without it behaving like a package? 

2.  Bundling seperate python modules to create a “Package”

“Currently, I have all of my modules in one folder, called python_modules and I have appended this path to os.path so I can easily import my individual modules as needed.”

“The __init__.py file is empty and does not have anything inside of it. The other modules all have various functions inside of them, and some are dependent on others. For example, network_functions.py relies on load_data_functions.py and parse_data_functions.py.”

3. How to structure a Python package so others can add modules easily

4.  How to organize multiple python files into a single module without it behaving like a package?

# lots of code in this 

5.  What's the difference between a Python module and a Python package?