Working with Dictionaries and ListsSets Modules you can use.pdf
- 1. Working with Dictionaries and Lists/Sets Modules you can use: argparse, reLinks, osLinks, collectionsLinks, sysLinks General Guidelines (Steps 1-6) You have more flexibility to implement your own function names and logic in these programs. The data files you need for this assignment can obtained from: HUGO_genes.txt, chr21_genes.txt Create an output directory inside your assignment4 directory called "OUTPUT" for result files, so that they will not mix with your programs. Output from your programs will be here! Pay close attention to how you'll run the run_lints.sh script (see below) Your program must implement command line options for the infiles it must open, but for testing purposes it should run by default, so if no command line option is passed at the command line, the program will still run. This will help in the grading of your program. Create a Python Module called called io_utils.py. Put this io_utils.py Module in a subdirectory named assignment4 inside your assignment4 top-level directory (see the tree below). Anytime a file needs to be opened (read or write) in your programs in this assignment, the program should call on this module's function get_filehandle. You can then use io_utils.get_filehandle by doing this at the top of your programs: from assignment4 import io_utils # I can then use the module's get_filehandle() function by: fh_in = io_utils.get_filehandle(infile1, "r") # note the function call "io_utils.get_filehandle()" You can also import this way (Either way is acceptable, but I will assume in this assignment you did it the way below. I think this is better for Pycharm) from assignment4.io_utils import get_filehandle # I can then use the module's get_filehandle() function by: fh_in = get_filehandle(infile1, "r") # note the function call "get_filehandle()" Your final submission must have the following files in bold and must use this directory structure. Make sure you put a blank __init__.py where I've denoted below, e.g.: assignment4/ assignment4 (see below) Make sure you have __init__.py only in assignment4/assignment4 folder, the tests folder, the unit folder, and not in the assignment4 main folder. Information on Source files The chr21_genes.txt file lists genes from human chromosome 21, in their order along the chromosome, as described in Hattori et al. (Nature 405, 311-319)Links to an external site.. For each gene, the file gives the gene symbol, description and category. The fields are separated by tabs. You will need to get the the meaning of each category. You can find these meanings in the original paperLinks to an external site., under the "Gene categories" section. Create a file named
- 2. chr21_genes_categories.txt that store this information in tab separated fields: This will be used in program #2 The HUGO_genes.txt file lists all human genes having official symbol approved by the HUGO gene nomenclature committeeLinks to an external site. (some have probably changed by now). For each gene, the file gives its symbol and description, separated by a TAB character. Exercises 1. Write a program (call it gene_names_from_chr21.py) that asks the user to enter a gene symbol and then prints the description for that gene based on data from the chr21_genes.txt file. The program should give an error message if the entered symbol is not found in the table (the user should should not have to worry about case, i.e. it will be a case-insensitive search). The program should continue to ask the user for genes until "quit" or "exit" is given (case-insensitive). Make sure to prompt the user to enter the quit to end the program. Use Dictionaries to solve this problem. HINT: Feel free to use as Dictionary of Dictionaries, but it is not required. HINT: First read the entire text file into a Dictionary that maps the association between gene symbol and description. Once again, make sure to use a Dictionary. Remember to have these command line options: $ python3 gene_names_from_chr21.py -i chr21_genes.txt Output from this program should just go to <STDOUT>: 2. Write a program (call it find_common_cats.py) that counts how many genes are in each category (1.1, 1.2, 2.1 etc.) based on data from the chr21_genes.txt file. The program should print the results so that categories are arranged in ascending order to an output file (call the output output OUTPUT/categories.txt . Read the paper to see what the categories represent and have this part of your output (this will be input from chr21_genes_categories.txt). Use Dictionaries to solve this problem. HINT: Feel free to use as Dictionary of Dictionaries, but it is not required. Note: you will notice that one gene has no category information. That's due to missing data in the file, JUST IGNORE THIS GENE!. Remember to have these command line options: $ python3 find_common_cats.py -i1 chr21_genes.txt -i2 chr21_genes_categories.txt Output to the file (OUTPUT/categories.txt) from this program: Note <Occurrence Here> is a number 3. Write a program (call it intersection_of_gene_names.py) that finds all gene symbols that appear both in the chr21_genes.txt file and in the HUGO_genes.txt file. These gene symbols should be printed to a file in alphabetical order (you can hard code the output file OUTPUT/intersection_output.txt) . The program should also print on the terminal how many common gene symbols were found. Use Lists or Sets to solve the problem. It is fine to use a temporary Dictionary to find the intersection of two Lists, but this can be simplified with Sets. Note: HUGO_genes.txt could have some duplicate entries. Remember to have these command line options: $ python3 intersection_of_gene_names.py -i1 chr21_genes.txt -i2 HUGO_genes.txt # the N 's below are an integer and bolded for illustration only
- 3. Number of unique gene names in chr21_genes.txt: N Number of unique gene names in HUGO_genes.txt: N Number of common gene symbols found: N Output stored in OUTPUT/intersection_output.txt STDOUT is shown above, and the actual output of the intersection goes to the file ( OUTPUT/intersection_output.txt) from this program: If you implemented intersection_of_gene_names.py correctly, this program could take any gene file that has the gene in the first column (even if it's the only column) (additional examples: hgnc_complete_set_reduced.txtLinks to an external site. and gene_age.txtLinks to an external site.) $ python3 intersection_of_gene_names.py -i1 hgnc_complete_set_reduced.txt -i2 HUGO_genes.txt Number of unique gene names in hgnc_complete_set_reduced.txt: 43547 Number of unique gene names in HUGO_genes.txt: 11815 Number of common gene symbols found: 8654 Output stored in OUTPUT/intersection_output.txt $ python3 intersection_of_gene_names.py -i1 gene_age.txt -i2 chr21_genes.txt Number of unique gene names in gene_age.txt: 307 Number of unique gene names in chr21_genes.txt: 285 Number of common gene symbols found: 4 Output stored in OUTPUT/intersection_output.txt You must solve exercises 1 and 2 by using Dictionaries, and exercise 3 using Lists or Sets