Programming in Bioinformatics - Block 3
I. Setting up Environment and Running the Code
- Create the environment using the pibi_block3.yml file with the command:
- conda env create -f pibi_block3.yml
- Activate it the following way:
- conda activate pibi
- Then run the code:
- python ex1.py
- python ex2.py
OR
- Run the batch script in order to also execute the STAR commands, tests, etc.:
- bash run_me.sh
II. Exercises
- Answers:
- Sequence 3 contains a 'D', making it invalid, so it was discarded.
- Sequence 1 and 2 are found on only one chromosome each.
- Sequence 4 on the other hand is found on three of the four chromosomes. However, this is likely due to its short size, rendering a hit not very meaningful.
- Answers:
- # of alignments: 108
- # of uniquely mapped alignments: 0
- # of multi-mapped alignments: 26
- The last point I did not know how to do, hence I can not say if the numbers match.
- Remark:
- My code coverage is not quite 100% since the main methods are not tested. However, I believe unit tests should not test them, which is why I left it as is.