[Bioperl-l] general question about possible attribute values

Florent Angly florent.angly at gmail.com
Wed Oct 24 17:25:25 EDT 2007


Dave,
Have a look in Bio::Assembly::Contig::IO, that's where all the supported 
assembly input/output formats are located. It's convenient to use the 
BioPerl Deobfuscator:
http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query 
<http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query>
'ace' and 'phrap' are the supported formats. The 'tigr' assembler format 
has been added in the CVS version recently too.
Florent


Dave Messina wrote:
> 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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> Bioperl-l at lists.open-bio.org
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>
>   



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