From: Christopher Dicely <cmdicely@...>
Date: 2008-02-23T00:52:33+09:00
Subject: Re: Bioruby-Name error: uninitialized constant

I get the same problem if I install with "gem install bioruby" (which
installs bioruby 0.6.4). If I do "gem install bio", which installs
bioruby 1.2.1, I don't have the problem.

(I didn't actually try loading anything, but
Bio::Alignment::MultiFastaFormat produces an uninitialized constant
error in the first case, and refers to a real class in the second.)


On Fri, Feb 22, 2008 at 2:58 AM, Carl Olme <calvin7602@hotmail.com> wrote:
> I'm very new to both programming in general and to programming in Ruby.
>
>  I have tried to write a programme in BioRuby:
>
>  require 'bio'
>
>  fasta = open('../sequence.fasta')
>  fasta_string = fasta.read
>
>  a = Bio::Alignment::MultiFastaFormat.new(fasta_string).alignment
>
>  a.each_site do|bases_at_site|
>           puts bases_at_site.join('')
>
>
>  When I run the programme in irb, I get the following output:
>
>  irb(main):001:0> require 'bio'
>  => true
>  irb(main):002:0>
>
>  irb(main):003:0* fasta = open('../sequence.fasta')
>  => #<File:../sequence.fasta>
>
>  irb(main):004:0> fasta_string = fasta.read
>  => ">ref|NT_039674.7|Mm18_39714_37:58262030-58293988 Mus musculus
>  chromosome 18 genomic contig, strain
>  C57BL/6J\r\nTTTCTATTTCAGCAGAAAAAAAAAAAGACGACTAGTCTTTGGGTT
>  #I cut out the rest of the file since it's very long.
>
>  irb(main):005:0>
>  irb(main):006:0* a =
>  Bio::Alignment::MultiFastaFormat.new(fasta_string).alignment
>  NameError: uninitialized constant Bio::Alignment::MultiFastaFormat
>         from (irb):6
>
>  irb(main):007:0>
>  irb(main):008:0* a.each_site do|bases_at_site|
>  irb(main):009:1*           puts bases_at_site.join('')
>
>  The solution is probably very simple, but I have played around with the
>  code for half a day now and can't get any further. I realise that the
>  problem is with how I have used Bio::Alignment, but not sure where I
>  have gone wrong.
>  --
>  Posted via http://www.ruby-forum.com/.
>
>