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Old 11-22-2010, 06:27 AM   #1
lskatz
Junior Member
 
Location: Atlanta

Join Date: Sep 2010
Posts: 9
Default How do I convert 454 ace to a regular ace?

I have read on the BioPerl site that a 454 ace is not standardized due to its coordinate system. How can I convert it to the standard ace file?

When I run this code either by using contig or assembly objects, I get an error.


PHP Code:
sub _newblerAceToAce($args){
  
my($self,$args)=@_;
  
my $ace454=Bio::Assembly::IO->new(-file=>$$args{ace454Path},-format=>"ace",-variant=>'454');
  
my $ace=Bio::Assembly::IO->new(-file=>">$$args{acePath}",-format=>"ace");
  
#while(my $contig=$ace454->next_contig){
  
while(my $scaffold=$ace454->next_assembly){
    print 
Dumper $scaffold;
  }
  return $
$args{acePath};

Code:
Can't call method "get_consensus_sequence" on an undefined value at Bio/Assembly/IO/ace.pm line 280, <GEN0> line 93349.

Further details:

From the bioperl site,
The ACE files produced by the 454 GS Assembler (Newbler) do not conform to the
reference ACE format. In 454 ACE, the consensus sequence reported covers only
its clear range and the start of the clear range consensus is defined as position
1. Consequently, aligned reads in the contig can have negative positions. Be sure
to use the '454' variant to have positive alignment positions. No attempt is made
to construct the missing part of the consensus sequence (beyond the clear range)
based on the underlying reads in the contig. Instead the ends of the consensus
are simply padded with the gap character '-'.

P.S. It'd be really awesome if there were perl tags on this forum but I couldn't find them in the help section. I'm using PHP tags as a substitute.
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