Python List Comprehension

Python list comprehension enables for easy manipulation of a list variable.  For example, list comprehension can be used to convert from a string to an integer or float as well as do some common operation on a list.  Below is an example script that shows the syntax for list comprehension and how to utilize the code in Python.  Hope its helpful.

Search for File Type in UNIX Directory and All Subdirectories

Here's a simple way to find and list all files in a UNIX directory and the containing subdirectories.  This example script shows how to search for all files with the extension ".R":

Is there a GWAS on that?

A great online resource to find whether a genome-wide association study (GWAS) has been published on a certain trait or disease is the National Human Genome Research Institute (NHGRI) webpage where they maintain a curated catalog of published GWAS.  Here trained curators are constantly scanning PubMed publications and other genomic resources looking for association studies linking a genomic position (usually a tagging SNP) to a disease trait of interest.  Details listed include study size, population, locus, risk allele, odds ratio, p-value, and other pertinent statistics.  Recently, the NHGRI in collaboration with the European Bioinformatics Institute (EBI) released an interactive version of the GWAS catalog called the GWAS Diagram Browser.  This provides a great way to visualize and filter many of the genome-wide significant findings from genome-wide associations studies.  Highlights include filtering by disease, time series views, and some useful downloads.

Another noteworthy resource is the HuGE Navigator GWAS Interagator.  This is a search tool similar to the NHGRI GWAS catalog, but more focused on a search terms.  Handy links are provided to other resources.  Of particular interest are links to visualize the variants in the UCSC Browser.

I am sure other GWAS resources exist as well, but these were the two main ones that first came to mind for me.  If you know other great GWAS resources capable of linking a genomic marker with a disease, please share in the comments below.

Genetic Simulation Resources

I just came across a useful repository of genetic simulation resources I thought would make a good addition to Genome Toolbox.  The site, aptly called Genetic Simulation Resources (GSR), provides a detailed listing of over 80 useful software applications available for genetic simulations.  The NCI sponsored catalog aids in scanning through available simulation programs, comparing similar applications, and quickly identifying the most appropriate software application for a particular study.  In addition to providing a description and external link, literature citations are also listed for many of the simulation packages.  If you are the developer of a genetic simulation resource that is not listed in the GSR repository, you can submit a request to add it.  Overall, a great resource for simulating data for genetic studies that may help you avoid reinventing the wheel by programming a de novo simulation routine.  A good first place to check.

Transpose List of Lists in Python

Today in Python I wanted to be able to transpose a list of lists that I created. So, for example, I wanted to be able to transpose the list

l=[[1,2,3],[4,5,6],[7,8,9]]

to this

t=[[1,4,7],[2,5,8],[3,6,9]]

I found an easy command to do this, where l is the list above and t is the transposed list.