[BioRuby] Bio::NCBI:REST:EFetch
Ben Woodcroft
donttrustben at gmail.com
Tue Jun 30 00:12:50 UTC 2009
Hi,
I was just googling how to download a genbank sequence using bioruby, and
somehow got pointed to this example code:
# == Usage
#
# Bio::NCBI::REST::EFetch.sequence("123,U12345,U12345.1,gb|U12345|")
But this doesn't seem to work in irb:
$ gem list bio
*** LOCAL GEMS ***
bio (1.3.0)
$ irb -rubygems
irb(main):001:0> require 'bio'
=> true
irb(main):002:0>
Bio::NCBI::REST::EFetch.sequence("123,U12345,U12345.1,gb|U12345|")
NameError: uninitialized constant Bio::NCBI::REST::EFetch
from (irb):2
Then I noticed by looking at the code I could just do
Bio::NCBI::REST::efetch("EF489424", {:rettype => 'fasta', :db =>
'sequences'})
So it seems there is some redundancy. What is going on? Should there be a
pointer to Bio::NCBI::REST::efetch from Bio::NCBI::REST::EFetch in the rdoc?
That would have made me understand a lot quicker, and I wouldn't have had to
look at the code to figure it out.
Thanks,
ben
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