Programming in Bioinformatics, Block 3

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

1. 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.

2. 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.

3. 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.