GEN220_2021

GEN220 2021 edition

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Homework 2

This assignment calls for two scripts. They are both started in the template.

Simple Count and Report

Write a program called squared_cubed.py and prints out three columns of data, ideally, separated by tabs. A header line should be written which is labels of the columns

N    Squared    Cubed

Column 1: numbers 0 -> 30 Column 2: Square (x^2) of column 1 Column 3: Cubes (x^3) of column 2

Output should look like this (but going up to at least 30 for for the N column)

N	Squared	Cubed
0	0	0
1	1	1
2	4	8
3	9	27
4	16	64
5	25	125

Genome Stats

We will compute some statistics for a tab delimited file called GFF which lists the location of genes and exons location in a genome annotation. Remember GFF is a structured format, tab delimited, which describes locations of features in a genome.

Recall eukaryotic Genes are made up of features: exons, introns, Untranslated regions (UTR). Some exons are coded as ‘CDS’ for CoDing Sequences - eg the ones that code for proteins.

See Wikipedia gene page and view of Gene structure in particular

Here is a GFF file for the Penicillium chrysosporium genome, which is the fungus which gave us one of the first antibiotics. The FungiDB database hosts genome sequences and data files for a collection of fungi.

The GFF file is available here FungiDB-54_PchrysosporiumRP-78.gff and FastA format genome assembly is FungiDB-54_PchrysosporiumRP-78_Genome.fasta. These are two files related to location of genes and sequence data.

Write a script called genome_stats.py to:

  1. Download these file (this can be in UNIX before you run your python script or you can incorporate this into the python). I already wrote part of this for you in the template code you can start with that executes a curl command from within your script. But if this doesn’t make sense to you, you can remove that.
  2. Print out the number of exons, CDS, protein_coding_gene features found in the genome annotation (GFF file)
  3. Compute and print out the total length of all the protein_coding_gene features (length is the END - START).
  4. Compute and print out total length of all the CDS features (length is the END - START).
  5. Use the FASTA file to compute the total length of genome (by adding up the length of each sequence in the file). Recall I lectured on a basic code to read in a FASTA file - you can also see that code template here, Print out the total length.
  6. Print out the percentage of the genome which is coding (using the numbers calculated from the protein_coding_gene)

Hints: