[Bioperl-l] Failed to load tigr xml files through Bio::Seq::tigr
jason.stajich at duke.edu
Fri Nov 4 11:30:39 EST 2005
Josh will have to chime in....
I don't know that Bio::SeqIO::tigr can parse all the different
flavors from TIGR, but I believe it was written particularly for the
rice data and maybe not for the version 3. Can you figure out what
is different in the version 3 over previous version of the TIGR
format? If I remember correctly the module was written with regexps
instead of an XML parser so I think it is pretty brittle to changes.
We may want to try and re-write it with XML::SAX or another XML
parser - I have written tigrxml for a different TIGR XML flavor in
this way. But we need someone to volunteer to help do this sort of
In this case I think you need to submit a bug rather than posting the
huge file to the mailing list. http://bugzilla.open-bio.org
On Nov 2, 2005, at 5:36 PM, Kun He wrote:
> Dear all,
> I have just tried to use the Bio::Seq::tigr module (BioPerl 1.5.1)
> to import information from TIGR Rice version 3 XML format
> pseudochromosome data, but it always failed on the loading
> (initiating) procedure.
> use strict;
> use Bio::SeqIO;
> my $file=shift;
> print $file,"\n";
> my $io = Bio::SeqIO->new(-file => "<$file", -format => "tigr" );
> There are a lot kinds of errors thrown out, based on different XML
> files. Attached is a sample xml from tigr, who can kindly help me
> to try if you can load it by the tigr.pm module? Thanks a lot!
> Kun He
[snip out XML, save bits!]
More information about the Bioperl-l