Parse fasta file

If you're like this you need to be careful because getting software to be "right", as compared to "right enough" is pretty hard. You might work hard doing something and find you never actually use it for anything, and that's just a waste of your time. Don't do things you aren't going to need.

If you know you only want a few fields from a file, only read those fields. If you have example data files you can check that they don't contain any surprises or special cases.

One thing you will need is a sanity check that the file is at least roughly what you expect it will be. Once you have an idea of what's in the file you need to figure out what you're going to do with the data.

For this lecture I'll have you write various filters to select or reject records based on the description and the sequence so you'll need to parse both of those fields. Some things are not well specified. The sequences are identical except for how the sequence is split across multiple lines. The first record has 60 characters per line while the second has The FASTA format doesn't specify exactly how many characters go in a line and different programs and people use different values.

I point this out because sometimes people like parsers to be "round-tripable". This means that the parser extracts enough information to reproduce the original file exactly. To make a round-tripable FASTA parser you would need to keep track of where the sequence line breaks occured.

I'll use an object model for each record. This style of design process is known as top-down design. Most programs are organized in layers. The top of the program is the main function, which calls functions which in turn call other functions. Python functions eventually depend on C functions which in turn depend on operating system functions which depend on hardware.

A good programmer needs to be be aware of all of the layers, which takes a long time to learn. Thankfully you can get work done without knowing everything! It's called top-down because I started with how the main function should look like and worked my way down. Another style is called bottom-up design which specifies each part and puts together parts to make larger and larger components. Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Warning Some features may not work without JavaScript. Please try enabling it if you encounter problems. Search PyPI Search. Latest version Released: Feb 13, The function above would run into trouble if the file was really big. If a file had more lines than the computer had memory, calling the function would result in a MemoryError. The open function does not actually read the file.

The file handle has a read function, which reads the entire content of the file into memory. If you called this function and the file was big enough you would run into a MemoryError. This is part of the reason this function is rarely used. It is also possible to process a file line by line by placing the file handle in a for loop. How might this be used in practise? Thanks nuin. However, this is exactly what I specified I wanted to avoid, for the reasons mentioned by Istvan Albert.

Then just change the return statement to a yield. The code needs to be modified to handle the first sequence. I guess you meant: change the items.

Because I teach biology students with no previous coding experience here is a code to read fasta that requires no understanding of somewhat more advanced things. It is by no means efficient for large files, but works for teaching purposes. If someone knows how to edit this to look like a code please do Login before adding your answer. Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Log In. Log In Sign Up About. Entering edit mode. Eric Normandeau 11k.