Camelia, the Perl 6 bug

IRC log for #bioruby, 2013-09-09

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All times shown according to UTC.

Time Nick Message
02:47 ngoto joined #bioruby
11:54 george__ joined #bioruby
11:55 george__ hello!
12:02 shevy hi george__
12:19 george__ am fine @shevy!
12:19 shevy hehe
12:19 shevy are you using ruby?
12:31 george__ yes I do use ruby
12:31 george__ a lot
12:31 george__ hehehe
12:33 shevy ok good!
12:33 shevy I too
12:34 shevy I dont use bioruby that much but I started to build my own stuff related to biology + ruby
12:35 george__ sounds cool
12:36 george__ what of things?
12:37 george__ i do use bioruby when i need to, particulary if i do proof of concept stuff
12:38 george__ so that i dont need to say create a  new method for a sequence class or read a phylo tree
12:38 shevy george__ my aim is to solve all biology-related problems with ruby in an automatable manner
12:38 george__ also lots of cool plugins are dependent on bioruby
12:38 shevy the biggest thing so far I built is mostly just a convenience IRB-like stuff.... in where I can do fun things
12:38 george__ for bio projects?
12:39 shevy assign ATCTG etc.. to assign a new DNA sequence... "convert" to translate this into aminoacids and complementary DNA strand... etc... etc..
12:39 shevy george__ yap
12:39 george__ mmh yeah got little scripts that do that for me as well
12:39 shevy next on my todo list is to do bioinformatics related things... comparing two sequences, scoring matches, blosum etc... etc..
12:39 george__ translate, revcomp
12:39 shevy george__ do you have a gem for your things?
12:40 george__ not yet
12:40 shevy ok
12:40 shevy my gem is very unfinished
12:40 shevy http://rubydoc.info/gems/bioroebe/0.0.2/frames
12:40 george__ they are scripts on my home dir symlinked to /usr/bin
12:40 shevy lacks documentation too, I Just released it to slowly get started
12:40 shevy I do something similar, but I use aliases instead
12:40 shevy so I dont have to symlink into /usr/bin
12:40 george__ yeah
12:41 shevy alias cua='$RUBY_SRC/bioroebe/codon_usage_analyzer.rb'
12:41 shevy class CodonUsageAnalyzer
12:41 george__ maybe would be nice to have a general purpose gem
12:41 shevy I love aliases
12:41 george__ say bio-utils
12:41 shevy george__ yeah ... but right now I am still only learning slowly
12:41 shevy yeah, I agree
12:41 george__ atually my folder is  so named
12:41 shevy but I think it must have good documentation so other people can use it too
12:42 shevy everyone is doing their own stuff, not many collaborate together, happens with bio-python too
12:43 george__ yeah
12:43 george__ i see
12:44 george__ and do you have proper option parsing
12:45 george__ it can  be cool to pull all of them into a folder and such that each little program does 1 and only 1 thing and share them
12:46 george__ but then some fuctionalities is  alredy available in say Emboss and like
12:47 shevy george__ hmm option parsing...
12:47 shevy I mostly pass ARGV to a method, as input
12:47 shevy and analyze it
12:47 shevy most classes I use are tiny and dont have many things that you can modify or change
12:47 shevy for something larger, I may have to use OptionParser or trollop or slop, I am not sure yet
12:48 shevy yeah george__
12:48 shevy I like simplicity
12:48 shevy when it is possible, I try to aim for simplicity... only when I really want to make it convenient, I try to make it more feature rich
12:55 george__ same case
13:12 george__ \join #nairobilug
13:45 george__ \NAMES #bioruby
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16:27 biorelated joined #bioruby

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