[BioRuby] Patch for Bug 18019.

[Naohisa GOTO]

On Wed, 14 Apr 2010 21:44:49 +0100
Jan Aerts <jan.aerts at gmail.com> wrote:

> Thanks for that, Anurag. Contributions to bioruby very much appreciated :-)
> 
> @Goto-san: can you merge that fix?

No, because the patch ignores reading of entries in the middle of the file.
To parse files distributed from NCBI, the delimiter should be "\n//\n",
and cannot be "\n//\n\n".

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

> 
> Cheers,
> jan.
> 
> On 14 April 2010 21:41, Anurag Priyam <anurag08priyam at gmail.com> wrote:
> 
> > Hello all,
> >
> > This is my start at being a part of the BioRuby developer community.
> >
> > The RubyForge bug tracking page shows bug 18019( GenBank each_entry, last
> > entry is always nil )[1] to be open. I am attaching a patch for it. Its
> > very
> > tiny. The fix was already suggested in a comment by Raoul Jean Pierre
> > Bonnal( the submitter of the bug ). I have verified the solution and
> > created
> > a patch for it. Or should I send a pull request on github?
> >
> > Patch( git format-patch ):
> >
> > >From ac82213651e5f5761d32cc9c658188d060c2e75a Mon Sep 17 00:00:00 2001
> > From: Anurag Priyam <anurag08priyam at gmail.com>
> > Date: Wed, 14 Apr 2010 22:58:45 +0530
> > Subject: [PATCH] fixed bug 18019: last entry of each_entry is nil
> >
> > ---
> >  lib/bio/db/genbank/common.rb |    2 +-
> >  1 files changed, 1 insertions(+), 1 deletions(-)
> >
> > diff --git a/lib/bio/db/genbank/common.rb b/lib/bio/db/genbank/common.rb
> > index 545eac1..eaa760c 100644
> > --- a/lib/bio/db/genbank/common.rb
> > +++ b/lib/bio/db/genbank/common.rb
> > @@ -24,7 +24,7 @@ class NCBIDB
> >  #
> >  module Common
> >
> > -  DELIMITER = RS = "\n//\n"
> > +  DELIMITER = RS = "\n//\n\n"
> >   TAGSIZE = 12
> >
> >   def initialize(entry)
> > --
> > 1.7.0
> >
> >
> > [1]
> >
> > http://rubyforge.org/tracker/index.php?func=detail&aid=18019&group_id=769&atid=3037
> >
> > --
> > Anurag Priyam
> > 2nd Year,Mechanical Engineering,
> > IIT Kharagpur.
> > +91-9775550642
> >
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> >
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