Programming in Bioinformatics, Block 3

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Miscellaneous pibi
Overview

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.
  1. 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.
  1. 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.
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