Mandatory Project 1

Project description

1. Design a data structure class phylogeny that represents a tree. Write a module that can parse a string in the newick tree format and represent this tree in your phylogeny data structure.

2. Write a suitable set of modules so that you can translate between any two of the following sequence formats both ways:
   • GDE (see also here.)
   • GenBank (see also here.)
   • Fasta , also called Pearson (see also here; scroll down to find the Fasta description.)

   You may assume that Fasta files are always DNA (or, if you want to, you can come up with some way of checking what type of sequence it is), and that the first word after the > is a unique identifier for the sequence. All modules should work with strings only; i.e. they should not handle reading/writing files (so the actual reading a file into a string or a list of strings is taken care of in a wrapper program; see below).

3. Write a wrapper program which handles interaction with the user and uses the above modules to translate between sequence formats.
   • The program should present the user with a menu like the following when started and then prompt the user for a choice:
     a) read sequence file, b) write sequence file, c) dna translation, d) write xml file, e) read newick file.
   • In case a) is chosen the user is presented with a new menu, namely a list of sequence formats which the program can handle.
   • After choosing one of these formats, the user is prompted for a file name. Then the file is read (catch any exceptions and give an error message), the appropriate filter is applied, and the sequences read are now represented somehow as 'current sequences'.
   • In case b) is chosen, the user chooses from the list of applicable formats and is prompted for a file name, and the current sequences are saved in one file in the chosen format. Give a suitable error message in case there are no current sequences.
   • In case c) is chosen, the user is prompted for a file name, and the current sequences are translated from DNA into amino acid sequences and written (in any form you wish) to the file. You may print the amino acid sequences to standard output as well if you like. If the current sequences are not DNA, the user is told so.
   • In case d) is chosen, the user is prompted for a file name, and the current sequences are saved in a file in XML format. Give a suitable error message in case there are no current sequences.
   • In case e) is chosen, the user is prompted for a newick tree file name. The file is read and the newick module is applied so that the tree is now represented using the phylogeny data structure as the 'current tree'.

Remarks

Since the formats do not keep the same information about a sequence, translating between them may force you to throw away some information while keeping some. It's up to you what you keep; our own internal format (Isequence.py) keeps the type, ID and name (if given) of a sequence along with the sequence itself. You may use and modify this format as you wish.

Documentation

The report should also include the full path to a directory in which all relevant program files (and nothing else) are located (thus if this directory and its content is copied, the programs will work when run from their new location). Make sure they are readable and don't change them after the deadline. Give instructions on how to run the main wrapper program.

Each program file should be easily readable Python code. I.e. put plenty of comments in the programs, use logical variable names, put in empty lines to delimit different parts of the program, etc. Don't explain the obvious ("here we use a for loop to go through all elements in the list"), just make sure everything is clearly understandable.

Your program should work on all the given sample sequences (see below). That means that if you translate, e.g., the sequences in GDE file 1 to Fasta, then to GenBank format, then back to GDE format, the actual sequences should match exactly the sequences in the original file (of course you may have lost some additional information on the way, but the sequences themselves should be unchanged).

Sample sequence files