[Bioperl-l] general question about possible attribute values

Dave Messina David.Messina at sbc.su.se
Wed Oct 24 16:59:12 EDT 2007


I couldn't find the formats for Bio::Assembly::Contig in any of the
documentation either.

In situations like these, I poke around in the code for methods that deal
with whatever I'm looking for. In this case, I went to the pdoc for
Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
_guess_format method:

sub _guess_format {

   my $class = shift;
   my $arg   = shift;


return unless defined($arg);
   return 'ace'
 if ($arg =~ /\.ace\.\d+$/i);
   return 'phrap'
 if ($arg =~ /\.phrap\.out$/i);

}

So it looks like 'ace' and 'phrap' are the two assembly formats that are
supported.

The other place where the question of formats often comes up is with
sequence formats. Those are better documented, in the SeqIO HOWTO:

http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats


Dave


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