[BioRuby] Fwd: Bio::NCBI:REST:EFetch

[Ben Woodcroft]

oops - forgot to post back to the mailing list.

---------- Forwarded message ----------
From: Ben Woodcroft <donttrustben at gmail.com>
Date: 2009/6/30
Subject: Re: [BioRuby] Bio::NCBI:REST:EFetch
To: Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp>


Hi,


> The NameError may be caused by old version of BioRuby which
> may exist somewhere in the $LOAD_PATH.


You are smart and I am stupid.

Both should work, and I think redundancy is not severe problem.
> Methods about EFetch is defined in Bio::NCBI::REST::EFetch::Methods
> and documents for the methods are also available.
>
> http://bioruby.org/rdoc/classes/Bio/NCBI/REST/EFetch/Methods.html
>
> But, the hierarchy of the documentation may be difficult to know
> for most users. Contributions and suggestions for documentation
> are welcome.


It is a bit misleading that they are redundant, but if they both work, then
I don't mind so much.

One suggestion I do have is that the returned objects shouldn't just be
strings, but should automatically be parsed. It seems redundant to call

Bio::FastaFormat.new(Bio::NCBI::REST::efetch("EF489424", {:rettype =>
'fasta', :db =>'sequences'})[0])

But it isn't too much of a big deal. In the end I've got my pipeline up and
bioruby is automating the things I want it to, so thanks!

ben




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