From ktym at hgc.jp  Mon Sep  3 10:11:40 2007
From: ktym at hgc.jp (Toshiaki Katayama)
Date: Mon, 3 Sep 2007 23:11:40 +0900
Subject: [BioRuby] Blast Format8 hsps' patch
In-Reply-To: <1188379270.9964.6.camel@localhost>
References: <1188379270.9964.6.camel@localhost>
Message-ID: <438ABF79-DB67-4DD2-B9D2-932C138C0BB0@hgc.jp>

Hi Raoul,

Thank you for pointing this bug out.

I think I fixed this problem but for double check,
could you personally send me your patch as a separate mail?
This list doesn't allow attachments.

Regards,
Toshiaki

On 2007/08/29, at 18:21, Raoul Jean Pierre Bonnal wrote:

> Hi Guys, 
> I found a bug in the parser. Take this example:
>
>
> contig00002     gi|15902044|ref|NC_003098.1|    99.71   1399    4
> 0       5       1403    414678  416076  0.0     2742
> contig00002     gi|118090026|ref|NC_003028.2|   98.25   858     5
> 1       556     1403    448891  449748  0.0     1592
> contig00003     gi|116515308|ref|NC_008533.1|   99.67   2997    7
> 2       1       2994    423818  426814  0.0     5848
> contig00003     gi|15902044|ref|NC_003098.1|    99.67   2997    7
> 2       1       2994    416288  419284  0.0     5848
> contig00003     gi|118090026|ref|NC_003028.2|   99.60   2997    9
> 2       1       2994    449959  452955  0.0     5832
> contig00004     gi|118090026|ref|NC_003028.2|   98.08   2238    40
> 3       5       2242    453000  455234  0.0     4072
> contig00004     gi|116515308|ref|NC_008533.1|   97.94   2238    43
> 3       5       2242    426859  429093  0.0     4048
> contig00004     gi|15902044|ref|NC_003098.1|    97.94   2238    43
> 3       5       2242    419329  421563  0.0     4048
>
>
> about last contig00003 the parser create an hit with 2 hsps, putting
> togheter results from last contig00003 and first contig00004, this is
> wrong. The code check only if the target is different from the prev one,
> in this case the target is the same but the query is different. 
>
> In attach the patch to solve the problem, I put a chk on the query too.
>
> Actually I don't know if the problem is present with other parsers.
>
> Best regards.
>
> --
> Ra
>
>
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby


From jan.aerts at bbsrc.ac.uk  Wed Sep 26 07:00:20 2007
From: jan.aerts at bbsrc.ac.uk (Jan Aerts)
Date: Wed, 26 Sep 2007 12:00:20 +0100
Subject: [BioRuby] Bio::Graphics on Rubyforge
Message-ID: <46FA3BC4.2020902@bbsrc.ac.uk>

All,

For those interested, I've just put a Bio::Graphics library on 
rubyforge. This library basically mimics the functionality of the 
Bio::Graphics library of BioPerl.
The website is http://bio-graphics.rubyforge.org

jan.

-- 
Dr Jan Aerts
Bioinformatics Group
Roslin Institute
Roslin EH25 9PS
Scotland, UK
tel: +44 131 527 4198
skype: aerts_ri

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From hien.le at mail.mcgill.ca  Wed Sep 26 11:17:39 2007
From: hien.le at mail.mcgill.ca (Hien Le)
Date: Wed, 26 Sep 2007 11:17:39 -0400
Subject: [BioRuby] GFF iterator feature
Message-ID: <20070926111739.huonhjcm00c4o80s@webmail.mcgill.ca>

Hello all,

I've been using Bio::GFF lately and couldn't seem to find a built-in 
way to iterate through the arrays of GFF lines. Am I missing something? 
Could future versions include such a feature?

For the moment, I've been adding an 'each' method to the class as follows:

class GFF < Bio::GFF::GFF3
  include Enumerable
  def each
    @records.each { |record| yield record }
  end
end

-H.