Assignment 2
Programming 3 & 4
Due Thursday 10/31 20:00
There are 12+2 points total (2 bonus points). I’d suggest that for each question, you create a program file (e.g. hw2_q1.py) and work on it till it is done. Once you finish all questions, copy and paste your answers to a file called “OmicsData_hw02_yourname.py” and mail it to 91085 through web teaching & learning platform of CAU. Please do your best to make sure your program can run.
• [4pt, 1 bonus] Get the following tab-delimited file from course server:
/mnt/scratch/yling/Genomis/Hw02/interactions.txt
This file contains four lines:
GeneA GeneB Lethality
g21 g102 0.9
g3041 g1 0.1
g21 g303 0.5
g93 g21 0.7
Write a python program that will:
• Take a string as argument so you can pass the file name “interactions.txt” to the program,
• Have try..except statements so if the file does not exist, it will print “ERR: file absent” and quit the program. [Hint: IOError]
• Go through the file (based on the argument passed) with a while loop,
• Get the names for GeneA and GeneB as well as the lethality with the split function,
• Count the number of pairs with lethality ≥0.5 and print out “Qualified pairs:” and the number of qualified pairs at the end, and
• Generate an space-delimited output file with the name output_yourname (e.g. output_LingYi) containing all gene pairs with lethality ≥0.5. You must use string formatting (Hint: %). The output file should look like:
GeneA GeneB
g21 g102
g21 g303
g93 g21
Comment on every line of your codes. You must close your input and output.
• [4pt, 1 bonus] Write a program that will:
• Read all lines in the file in question 1 into a list (must use the readlines function) called line_list.
• Use a for loop to go through line_list,
• Store gene names and lethality values in a dictionary called pair_dict where:
• The key is GeneA and,
• Its corresponding value is a list of GeneBs that interact with the GeneA in question.
• The dictionary should looks like:
{“g21”:[“g102″,”g303″],”g3041”:[“g1″],”g93”:[“g21”]}
• At the end of the program, print out the dictionary with the print command.
Comment on every line of your codes.
• [4pt] Let’s create a nested dictionary called new_dict:
• Assume that you have already created the line_list that is a list with all the lines in the interaction.txt file.
• In the dictionary:
• The key is a gene X (can be in the GeneA or GeneB column, so there should be six keys at this level),
• Its corresponding value is another dictionary where:
• The key is a gene that interact with gene X
• Its corresponding value is lethality converted into a floating point number.
• So this nested dictionary looks like:
{“g21” :{“g102” :0.9,
“g303” :0.1,
“g93” :0.7},
“g102” :{“g21” :0.9},
“g303” :{“g21” :0.5},
“g3041”:{“g1” :0.1},
“g1” :{“g3041”:0.1}
“g93” :{“g21” :0.7}
}
• Note that for example g21 have two entries as GeneA and one entry as GeneB in the file. So the value corresponds to g21 should contain three genes.
• At the end of the program, print out the dictionary with the print command.
Comment on every line of your codes.