Refactor logic to read trees from multiple formats into a function #310
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Adds a new function `read_tree` to the `utils` module that tries to safely handle reading trees in multiple input formats. This kind of try/except approach to loading trees is necessary because Bio.Phylo.read requires a specified tree format, but we do not know the format of a given tree by the filename extension alone. A side effect of this commit is that missing input files are also now properly caught and reported to the user on the command line instead of raising a Python exception. Closes #302.
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This is great @huddlej, thanks! To add a little more clarity for anyone following this, the issue with my previous fix was that it cycles through checking both 'newick' and 'nexus' format, and thus if you exit on an exception from not being able to read newick, you never try to read nexus. John's new code gives us a great way to standardise reading in trees and checking all the stuff we should! |
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Turned into 🎉 big win. Thanks @huddlej |
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Adds a new function
read_treeto theutilsmodule that tries to safelyhandle reading trees in multiple input formats. This kind of try/except approach
to loading trees is necessary because Bio.Phylo.read requires a specified tree
format, but we do not know the format of a given tree by the filename extension
alone.
A side effect of this commit is that missing input files are also now properly
caught and reported to the user on the command line instead of raising a Python
exception.
Closes #302.