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Ruby, JRuby, Rails, the whole disaster

ruby-perf-src.zip

Source code for ruby benchmarks and support file.

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ruby-conc.xls

Ruby performance results.

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Benchmarking

Some quick tests of Ruby's speed and concurrency.

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Consensus in BioRuby

Explaining the ill-explained ways to obtain a consensus sequence in BioRuby.

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checkseqs.rb

A BioRuby to check sequences for ambiguous characters and clean them up.

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Cleaning biosequences

A simple script to check and purge sequence files of possible problems.

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sumsnps.rb

A simple script to find and save SNPs within an alignment.

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Summarizing SNPs

A simple script to count and save SNP data from an alignment.

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Drawing sequence logos

A very simple script to do a simple but tedious task.

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Illogical or

In which we consider the difference difference between “or” and “||” in Ruby

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Fetch sequences from db

A simple script to grab bioseqs by accession.

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The Genbank parsing problem

Oh BioRuby, you are just as capricious and inconsistent as Ruby itself.

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