Ettema lab blog

Finding overlapping ranges in Perl

Finding if a value is in a range is something you come across quite often. For instance, perhaps you want to see if a sequence is in a particular region. Or in my case it is to find if two genes overlap. One could solve this in a lot of different ways, but the one

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Extracting information from GenBank files

Sometimes you want to get a quick overview of the distribution of a group of uncultured microorganisms. In my case I had extracted all the 16S sequences classified as a certain clade, from the Silva database, and I wanted to know which environment they came from. This information can easily be found in the GenBank

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Stricter strict and warnings

I try to always make sure to have the modules strict and warnings in every perl script I make. Of course that means 2 lines of code

A nice module to replace these with is ‘strictures’. Basically it sets both strict and warnings, with the added benefit of making all warnings fatal.

This

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