fasta_project

First public release of the FASTA project! Current state: finished!

Description of the project:

This is a project made for the Programming II course. It provides a series of scripts for manipulating and representing FASTA sequences and .fasta files, which are files in a text-based format, used for representing nucleotide sequences of amino acid base pairs. We use OOP to create sequence objects, that store identifiers and their nucleotid sequences. On top, multiple classes allow manipulation of sequences for various purposes.

Scripts:

The project has a total of 5 scripts, each with different functionalities.

• fasta_format.py: allows for simple text formatting of .fasta files, like upper or lower case, and inserting newlines for defining specified line lenghts.

• disambiguate.py: manages transformations of repeated sequences in .fasta files. Allows for the elimination of sequences with repeated identifiers or their renaming.

• reverse-complement.py: this script implements sequence transformations such as reversing sequences or substituting each nucleic acid with it's complementary.

• multiple_transformations.py: allows to combine all transformations in the disambiguate.py and reverse-complement.py scripts.

• fasta_summary.py: provides a script for making simple statistical analysis of a .fasta file. Allows to export .csv files with the number of occurences of each nucleic acid, and produce data analysis images for appearance of each acid over total sequence length and for frequency of appearance of each sequence's length. Works both with .fasta files and with directories containing them.

Installation:

For correct usage now the user should add the project directory to the environment variable PYTHONPATH so that Python knows where to search for the executable files.

One way of doing it is this, do the following after downoading the project:

• Go, through command line, to the root directory in which the project was downloaded in your PC. For example if you downloaded it to C:\user\documents, go to C:\user\documents\fasta_project.

• Once there, you must add the path to the environment variable. In Windows, type the followng command: $env:PYTHONPATH = '.' On Linux, type: export PYTHONPATH=.

• Of course, the same would work if '.' is substituted with the absolute path of the directory.

• This must be done each time the terminal is opened to use the project, since the environment variable dissapears after closing it.

• After that, experiment with the sample commands that are listed in the script modules's docstrings. You will need .fasta files to manipulate. You can generate them online, save them in a .txt or other file format, and just rename them to the .fasta extension. Beware that the sequences in the file can only contain the following uppercase letters: A, C, T, G.