Parsing genbank files

This allows for extraction of various types of sequences, including amino acid and spliced transcripts. AnnotationCollections have the ability to be subsetted. BioCantor latest. NoncodingTranscriptError is raised when trying to convert CDS coordinates on a non-coding transcript tx1. Ask Thomas if you want some areas to be expanded upon. Biopython is an amazing resource if you don't feel like figuring out how to parse a bunch of different idiosyncratic sequence formats fasta,fastq,genbank, etc.

Here I focus on parsing Genbank files; SeqIO can be used to parse a bunch of different formats, but the structure of the parsed data will vary. Let's say you want to go through every gene in an annotated genome and pull out all the genes with some specific characteristic say, we have no idea what they do. This problem is pretty easy once you know how to use Biopython's data structures. For this example I will be using the E. To begin, we need to load the parser and parse the genbank file.

It should only take a couple seconds. Use SeqIO. Since we're using genbank files, there typically I think only be a single giant sequence of the genome. There are a bunch of data objects associated to the parsed file. The main one of interest will be the features object, which is a list of all the annotated features in the genome file. Features contain all the annotation information that you care about. Biopython has a somewhat confusing object structure, so let's step through what types of information a feature can have.

The easiest way to inspect the structure of some random object I have found is Ipython , which is an awesome python interpreter that also has some nice terminal features like cd ls mv After using this interpreter for a year, I hate going back to the vanilla one. Its best feature for my forgetful mind is easy access to help files associated with functions, and the objects associated with a class. In case you didn't catch it in the above, here's how to get the sequence information and the secondary structure element information.

I think the quotes are part of the syntax of the file format and aren't part of the actual data. Oh well. For the assignment you'll need to know one more Python feature. So far your programs have used a hard-coded filename for input data. I'll want you to take a name from the command-line. These values are available to Python progams using the sys. That's has a list of all the parameter strings passed on the command line.

The first argument sys. It's the actual name of the program being run.