Description
The purpose of this exercise is to get you prepared to write convenience wrapper scripts that run 3rd party
software tools for performing alignment, assembly, phylogeny inference, secondary structure prediction, etc.
You will learn how to write a script in Python that uses command-line parameters, reads a file, and can
execute a command and retrieve its standard output and error output. You must be using a linux
operating system to complete this assignment.
Tasks
1. Download the Homework1 folder: https://www.dropbox.com/s/lw8a5l4g6b9yfjv/Homework1.zip?dl=1
2. Modify Homework1/template.py for Python 2 or Homework1/template-python3.py for Python 3 to do
the following:
a. Call the BURST command from within python using the following syntax:
./burst -r ref.fna -q query.fna –taxonomy taxonomy.txt -o output.txt
b. Print out the return value, standard output, standard error.
3. Verify that your program runs with:
python homework1.py -q query.fna -r ref.fna -t taxonomy.txt -c /path/to/burst -o output.txt -V
4. The output file shows information for every query sequence that hit a reference sequence at 97%
similarity or above. Answer these questions, using this guide to the meaning of the first 12 columns
in the output.txt file: https://github.com/seqan/lambda/wiki/BLAST-Output-Formats. The 13th column
shows the taxonomic assignment of each query sequence.
a. What fraction of the original input query sequences had a match in the database at 97% or
above? Note that a few matches fell below 97%. You can exclude these. Inspect query.fna,
which is in FASTA format, to ensure that you are counting the correct number of input
sequences.
b. What is the most common bacterial species in the query set? Note that any taxonomy string
ending with something after the last “s__” is a species name. If a string ends with “s__” and
nothing else, then it was ambiguous and does not count as a species.
c. What is the average percent similarity of the matches? You can exclude those below 97%.
Deliverables
1. Please turn in, via moodle:
a. Your well-commented code. Note in your code the names of any people with whom you
discussed the assignment. This includes code for answering question 4 above.
b. The output printed by your program (this is what is printed to standard out, not the BURST
output file).
c. The output.txt file generated by BURST
d. Answers to questions above in txt/doc/pdf
