Write a program (call it intersection.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 us
Write a program (call it intersection.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.py -h usage: intersection.py [-h] -i1 FILE1 -i2 FILE2 Provide two gene list (ignore header line), find intersection optional arguments: -h, --help show this help message and exit -i1 INFILE1, --infile1 INFILE1 Gene list 1 to open -i2 INFILE2, --infile2 INFILE2 Gene list 2 to open
$ python3 intersection.py -i1 chr21_genes.txt -i2 HUGO_genes.txt # the N's below are an integer and bolded for illustration only
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:ABCG1 ADAMTS1 ADAMTS5
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... If you implemented intersection.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.txt (Links to an external site.) and gene_age.txt (Links to an external site.))
$ python3 intersection.py -i1 hgnc_complete_set_reduced.txt -i2 HUGO_genes.txt # the N's below are an integer and bolded for illustration only
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.py -i1 gene_age.txt -i2 chr21_genes.txt # the N's below are an integer and bolded for illustration only
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
- Pay attention to the outputs above
- Do not forget to implement the my_io.py module and place that in a subdirectory of assignment4, i.e. assignment4/assignment4/my_io.py
- Whenever you need to open a filehandle in any of your programs the code should call the my_io.get_fh function frommy_io.py
- Make sure to include documentation for the my_io.py module
- Make sure to include the __init__.py (see above)
- Do not forget to implement the test_my_io.py test script and put that in a subdirectory of assignment4, i.e. assignment4/tests/unit/test_my_io.py
- create a .coveragerc file in the working directory like I showed you above and submit that with your final submission
- To receive credit for your test_my_io.py, you must achieve coverage >=70%.
- Use relative paths for outputs, i.e. do not use absolute paths like: /home/your_user_name/programming6200/assignment4/OUTPUT
- Instead, use relative paths like outfile = "OUTPUT/intersection_output.txt"
- Make sure your programs run with defaults on Defiance, but also have the options provided above
- HINT: If you use the same data structure in problems 1 and 2 (like a Dictionary of Dictionaries) or have the same code to get the data, wrap it up in another Module.
- This is not required, but great practic
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