[Bioperl-l] general question about possible attribute values

Joseph Fass joseph.fass at gmail.com
Wed Oct 24 17:45:29 EDT 2007


thanks, both of you!

On 10/24/07, Florent Angly <florent.angly at gmail.com> wrote:
>
> 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
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


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