Contents

Tutorial 6

Question 1

In this question you will use data from a star catalogue to create a picture that plots the locations of stars, like this:

../_images/star_map.png

First download the two files:

stars.csv Cas_lines.txt

The file stars.csv contains one line for each star that is represented in the catalogue. The meaning of each field (column) is described below.

  • The first three fields are the x, y and z coordinates for the star. We will ignore the z coordinate, and use only the x and y coordinates. Each axis in the coordinate system goes from -1 to +1, and the centre point is 0,0.

  • The fourth field is the Henry Draper number, which is simply a unique identifier for the star.

  • The fifth field is the magnitude (or brightness) of the star.

  • The sixth field exists only for a small number of stars and is a semicolon-separated list of names for a star. A star may have several names.

  • The fields that you will need for this assignment include the x and y coordinates, the magnitude and the name of each star.

Step 1

  • Create four empty lists x, y, mag and star_name to store the x coordinate, y coordinate, magnitude and star name of each star.

  • Open the file stars.csv and use csv.reader to load the contents into the four lists. Make sure you convert each to the appropriate data type (float or string).

  • Where there is more than one star name, store the second one (using string.split and string.strip)

Step 2

Make a scatter plot of the x, y coordinates. Use the following code to set up your plot:

fig, ax = plt.subplots(figsize=(5,5))
fig.patch.set_facecolor("black") # set the figure background to black
ax.axis("off") # remove the axes
ax.set_facecolor("black") # set the plot background to black

Use ax.scatter(x, y) to plot the stars. Try to make it look similar to the image above by passing suitable values for the marker, s and color parameters (see https://matplotlib.org/3.3.3/api/_as_gen/matplotlib.pyplot.scatter.html).

Step 3

The file Cas_lines.txt contains two star names per line. Each pair of star names represent one line to be drawn for the constellation. Write code which iterates over each line in the file, and for each line, determines the x and y coordinates of the two stars, then draws a line between them on the plot.

The following code will plot a line between coordinates (x_1, y_1) and (x_2, y_2).

ax.plot([x_1, x_2], [y_1, y_2])

  • Open the file Cas_lines.txt and use csv.reader to iterate over each row. For each row:

    • use star_name.index to find the index of the two star names in the list of star names you created in step 1.

    • determine the x and y coordinates of each

    • use the code above to plot a line between them.

Question 2

Ps_kr_G2B.fasta

In a previous worksheet you wrote a Python script which converted a RNA sequence into a protein by performing the translation (RNA -> amino acid sequence) process. In this question you will extend the script to:

  1. Read a DNA sequence from a fasta file

  2. Transcribe the sequence (convert from DNA to RNA) by replacing all occurrences of “T” with “U”.

  3. Translate the sequence (already done last week)

  4. Count the frequency of each amino acid and plot it as a histogram

../_images/aa_freq.png

Step 1

Write a script which opens the file Ps_kr_G2B.fasta and reads the DNA sequence into a string variable. Make sure you discard the line beginning ‘>’ and remove newline characters.

Step 2

Convert the DNA sequence to an RNA sequence using string.replace to replace each occurrence of T with U. (e.g. “CTGCTC” should become “CUGCUC”).

Step 3

Translate the RNA sequence to a protein by generating a string variable containing the amino acid sequence (you can reuse last week’s code).

Step 4

Write a script which creates a list which contains the number of occurrences of each amino acid in the protein. Plot a histogram showing the frequency of each amino acid. Add y-axis label ‘Frequency’ and x-axis label ‘Amino acid’.