Homework 3

Please create a github called TRGN510_Assignment3.

It should contain 3 scripts called circumference.py, area_code.py, and gene_names.py.  Please submit the github repository as a URL to the blackboard homework.

1. Create a basic python script called circumference.py that assigns pi to 3.14159 and prints the circumference of a circle given a second variable radiuswith the initial value of 3.  In this example, the radius should be assigned within the script.  The output should print The circumference of a circle of radius 3 is ??? where ??? is the answer following 2*pi*r
2.  Create a script area_code.py which reads a file of phone-numbers such (602)-232-2322 and prints out the area codes (such as 602) for each line of the file.
3. Create a script called gtf2json.py. For this script, you’ll need to have access to a dataset and I would like you to put the dataset in a different directory.  First, download the file, Homo_sapiens.GRCh37.75.gtf.gz, from http://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens using wget, and place this file within a directory called data within your home directory. Unzip this file with gunzip, gunzip Homo_sapiens.GRCh37.75.gtf.gz  The command head ~/data/Homo_sapiens.GRCh37.75.gtfshould give the start of the file (#!genome-build GRCh37.p13). Next, create a python script called gtf2json.py that takes a gtf file (which you downloaded one of them) as an argument, and spits out the gene_name, the chromosome (the first column), the starting position (the fourth column), and the ending position (the fifth column) for only those columns where the third column is “gene”.  Columns within the file are tab-delimited. The result should be JSON format:

   ./gtf2json.py ~/data/Homo_sapiens.GRCh37.75.gtf
   [
     {"geneName":"OR4G4P","chr":"1","startPos":52473, "endPos":54936},
     ... 
   ]
   

   You do not need to have the GTF within your repository.  Only the link should be in your README.