[Bioperl-l] question about Bio::DB::GFF

xianran li xianranli78 at yahoo.com.cn
Mon Sep 3 22:11:09 EDT 2007


 
  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

       
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