Downloading data files to your computer

import cogent3

url = "https://replace with the full url to the file"
aln = cogent3.load_aligned_seqs(url)
aln.write("som/local/path.fa")

Several sections have sample data files for you to work on. The cogent3.loading... functions can read content from urls. They will return a cogent3 object which has a write() method that can be used to save the data locally. The above example is for downloading an alignment. To get the url, you need to right+click (or control+click) on the web page link and select “copy link”. Paste that into your notebook as per above.

Note

Since the filename suffix is used to identify the file format, make sure the local filename has the same suffix as the original.

8. Molecular Evolutionary Analyses Using cogent3

We have focussed, thus far, on developing an understanding of programming logic and then applied that to tackling basic algorithmic tasks in sequence comparison. While this skill is invaluable, there is an advantage to using existing tools designed for manipulating the data types that define the fundamental structures in the analysis of biological data. Combining your developing skills in programming with familiarity of important domain specific tools, you greatly expand the range of problems you can address. You will find cases where are able adapt existing tools to solving problems for which there is no current solution.

cogent3 is just such a library for analysis of genomic sequences. Just as numpy provides critical capabilities for solving numerical computational problems, cogent3 provides the analogous tools for handling biological data and certain categories of analysis.

cogent3 is a Python library for handling genomic data with particular strengths in statistical analysis of genomic divergence. It provides tools for loading standard data formats, manipulation of biological data, statistical modelling (including standard statistical tests). These will be introduced via introduction to the major data types and concepts.

Note

See cogent3 for the full project documentation. We will link to specific sections as appropriate.