From hs568 ＠ cornell.edu  Thu Feb 11 06:53:12 2010
From: hs568 ＠ cornell.edu (Haruo Suzuki)
Date: Wed, 10 Feb 2010 16:53:12 -0500
Subject: [Glang-devel] =?iso-2022-jp?b?VEFYT05PTVkbJEIkTk5jMzA9aE19GyhC?=
Message-ID: <50A37DEC-1D5F-4ECE-8E6D-6B295CAC8893@cornell.edu>

一部の原核生物（Bacillus, Streptococcus, Staphylococcus,  
Synechococcus）で、GenBankファイルの分類群の情報が欠損 
しています。

G/IO/GenBankI.pm
の
     $this->{HEADER} =~ /((Archaea|Bacteria|Eukaryota);.*?)\n\S/s;
     $this->{TAXONOMY}->{0} = $1;
     $this->{TAXONOMY}->{0} =~ s/\n//g;
     $this->{TAXONOMY}->{0} =~ s/\s+ / /g;
     $this->{TAXONOMY}->{0} =~ s/; /;/g;
の後に
$this->{TAXONOMY}->{0} =~ s/Bacillales/Bacilli;Bacillales/;
$this->{TAXONOMY}->{0} =~ s/Lactobacillales/Bacilli;Lactobacillales/;
$this->{TAXONOMY}->{0} =~ s/Staphylococcus/ 
Staphylococcaceae;Staphylococcus/;
$this->{TAXONOMY}->{0} =~ s/Synechococcus/ 
Synechococcales;Synechococcaceae;Synechococcus/;
を加えることにより修正できます。

以下のファイルで確認しました。
$file = 'NC_000964.gbk'; # Bacillus subtilis subsp. subtilis str. 168
$file = 'NC_004116.gbk'; # Streptococcus agalactiae 2603V/R
$file = 'NC_002951.gbk'; # Staphylococcus aureus subsp. aureus COL
$file = 'NC_007604.gbk'; # Synechococcus elongatus PCC 7942

Haruo Suzuki, Ph.D.
Department of Population Medicine and Diagnostic Sciences
College of Veterinary Medicine
Cornell University
Ithaca, NY 14853, USA
TEL: +1-607-253-4228
E-MAIL: hs568 ＠ cornell.edu


From gaou ＠ sfc.keio.ac.jp  Thu Feb 11 10:56:34 2010
From: gaou ＠ sfc.keio.ac.jp (Kazuharu Arakawa)
Date: Thu, 11 Feb 2010 10:56:34 +0900
Subject: [Glang-devel] =?iso-2022-jp?b?VEFYT05PTVkbJEIkTk5jMzA9aE19GyhC?=
In-Reply-To: <50A37DEC-1D5F-4ECE-8E6D-6B295CAC8893@cornell.edu>
References: <50A37DEC-1D5F-4ECE-8E6D-6B295CAC8893@cornell.edu>
Message-ID: <3BE03F78-172B-4C4C-9E3B-D2CECCC796F1@sfc.keio.ac.jp>

g.

ありがとうございます、mergeしました。


On 2010/02/11, at 6:53, Haruo Suzuki wrote:

> 一部の原核生物（Bacillus, Streptococcus, Staphylococcus,
> Synechococcus）で、GenBankファイルの分類群の情報が欠損
> しています。
>
> G/IO/GenBankI.pm
> の
>     $this->{HEADER} =~ /((Archaea|Bacteria|Eukaryota);.*?)\n\S/s;
>     $this->{TAXONOMY}->{0} = $1;
>     $this->{TAXONOMY}->{0} =~ s/\n//g;
>     $this->{TAXONOMY}->{0} =~ s/\s+ / /g;
>     $this->{TAXONOMY}->{0} =~ s/; /;/g;
> の後に
> $this->{TAXONOMY}->{0} =~ s/Bacillales/Bacilli;Bacillales/;
> $this->{TAXONOMY}->{0} =~ s/Lactobacillales/Bacilli;Lactobacillales/;
> $this->{TAXONOMY}->{0} =~ s/Staphylococcus/
> Staphylococcaceae;Staphylococcus/;
> $this->{TAXONOMY}->{0} =~ s/Synechococcus/
> Synechococcales;Synechococcaceae;Synechococcus/;
> を加えることにより修正できます。
>
> 以下のファイルで確認しました。
> $file = 'NC_000964.gbk'; # Bacillus subtilis subsp. subtilis str. 168
> $file = 'NC_004116.gbk'; # Streptococcus agalactiae 2603V/R
> $file = 'NC_002951.gbk'; # Staphylococcus aureus subsp. aureus COL
> $file = 'NC_007604.gbk'; # Synechococcus elongatus PCC 7942
>
> Haruo Suzuki, Ph.D.
> Department of Population Medicine and Diagnostic Sciences
> College of Veterinary Medicine
> Cornell University
> Ithaca, NY 14853, USA
> TEL: +1-607-253-4228
> E-MAIL: hs568 ＠ cornell.edu
>
> _______________________________________________
> Glang-devel mailing list
> Glang-devel ＠ lists.sourceforge.jp
> http://lists.sourceforge.jp/mailman/listinfo/glang-devel