Archive For The “programming” Category

Favorite atom packages

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hydrogen atom-beautify autocomplete-python busy-signal goto-definition highlight-selected linter-flake8 markdown-writer minimap python-autopep8 symbols-tree-view script ftp-remote-edit

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ipython notebooks

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ipython notebooks are a useful way to run/save a session of python code/analysis. I can see it as a useful way to share code and promote reproducible research. In several respects, its similar to knitr in R except that it runs in your browser. I’ve been using ipython notebook on our cluster, which turns out…

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local lib for perl

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Using shared environments has it benefits, but dealing with perl install paths isn’t one of them. You can install perl to a local directory, but i’ve since found the local::lib module to be a great means of isolating a perl install similar to python’s virtual environment. The basics: download the locallib source, unpack and change…

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bioperl for sequences

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There are a lot of ways of dealing with sequence data, but I still like the venerable bioperl. It’s just a pain to remember the syntax all the time. So here’s a quick reminder for how to deal with Fasta sequences. Your fasta file can have just one sequence or more than one sequence, separated…

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