[Bioperl-l] =?gb2312?q?=BB=D8=B8=B4=A3=BA=20Re:=20=20question=20about=20Bi?= =?gb2312?q?o::DB::GFF?=

xianran li xianranli78 at yahoo.com.cn
Tue Sep 4 00:58:48 EDT 2007


Hi, everybody,
   
  It looks like for the different perl version(5.8.8 of  windows and 5.8.5 for linux). And I fixed this problem by adding ";Name=XXXX" after each line with "mRNA"
  ##############################################################################
  Chr01 bgf mRNA 18113 20165 . + . ID=BGIOSIBCE000001.1;Name=BGIOSIBCE000001.1
Chr01 bgf CDS 18113 19150 . + 0 Parent=BGIOSIBCE000001.1
    ##############################################################################

  This time my code works properly.
   
  Xianran

Chris Fields <cjfields at uiuc.edu> дµÀ£º
  Not sure if the gff3 you show was modified for demonstration here but 
it should always be tab-delimited. Also, I have had problems myself 
when using files with Windows/Mac Classic line endings on UNIX'y 
systems (Excel and a few other Mac OS X programs insist on adding \r 
instead of \n, which plays havoc with parsers sometimes even with 
readline fixes).

chris

On Sep 3, 2007, at 9:11 PM, xianran li wrote:

>
> Hi,
>
> I tried to load the gff3 file with load_gff.pl and extrac some 
> information with Bio::DB::GFF. Althougth this code work properly 
> under windows xp, the $seg got nothing when i run it under Linux.
>
> Here is my code and the gff3 file,
> ####################################################################
>
> #!/usr/local/bin/perl -w
>
> use strict;
> use Bio::SeqIO;
> use Bio::DB::GFF;
>
> my $in_gff = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt',
> -dsn => 'dbi:mysql:test',
> -aggregator => ['coding'],
> -user => "lixr",
> -pass => "123456"
> );
> my $seg = $in_gff->segment'BGIOSIBCE000001.1');
> print $seg->abs_start."\n";
>
>
> ##################################################################
> ##gff-version 3
> ##sequence-region Chr01 1 43037
> Chr01 bgf mRNA 18113 20165 . + . ID=BGIOSIBCE000001.1
> Chr01 bgf CDS 18113 19150 . + 0 Parent=BGIOSIBCE000001.1
> Chr01 bgf CDS 19344 20165 . + 0 Parent=BGIOSIBCE000001.1
> Chr01 bgf mRNA 30220 36442 . + . ID=BGIOSIBCE000002.1
> Chr01 bgf CDS 30220 30387 . + 0 Parent=BGIOSIBCE000002.1
> Chr01 bgf CDS 31128 31226 . + 0 Parent=BGIOSIBCE000002.1
> Chr01 bgf CDS 32228 32331 . + 0 Parent=BGIOSIBCE000002.1
> Chr01 bgf CDS 33907 34715 . + 1 Parent=BGIOSIBCE000002.1
> Chr01 bgf CDS 34799 34921 . + 2 Parent=BGIOSIBCE000002.1
> Chr01 bgf CDS 35003 35091 . + 2 Parent=BGIOSIBCE000002.1
> Chr01 bgf CDS 35179 35379 . + 0 Parent=BGIOSIBCE000002.1
> Chr01 bgf CDS 35981 36442 . + 0 Parent=BGIOSIBCE000002.1
> Chr01 bgf mRNA 38143 39015 . - . ID=BGIOSIBCE000003.1
> Chr01 bgf CDS 38143 38541 . - 0 Parent=BGIOSIBCE000003.1
> Chr01 bgf CDS 38649 38813 . - 0 Parent=BGIOSIBCE000003.1
> Chr01 bgf CDS 38917 39015 . - 0 Parent=BGIOSIBCE000003.1
> Chr01 bgf mRNA 39545 42080 . + . ID=BGIOSIBCE000004.1
> Chr01 bgf CDS 39545 40584 . + 0 Parent=BGIOSIBCE000004.1
> Chr01 bgf CDS 40677 41042 . + 1 Parent=BGIOSIBCE000004.1
> Chr01 bgf CDS 41130 41208 . + 1 Parent=BGIOSIBCE000004.1
> Chr01 bgf CDS 41740 41920 . + 0 Parent=BGIOSIBCE000004.1
> Chr01 bgf CDS 42037 42080 . + 2 Parent=BGIOSIBCE000004.1
> #################################################################
>
>
> I would appreaciate if any one can give me some clues/link to 
> accomplish this.
>
> thanks in advance ,
>
> Xianran Li
>
>
> ---------------------------------
> ÑÅ»¢ÓÊÏ䣬ÒÔ°²È«Öø³Æ£¬ÊÇÖµµÃÐÅÀµµÄÓÊÏäר¼Ò£¡
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





       
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