[Bioperl-l] Error parsing TIGR xml

[Jason Stajich]

I didn't submit tigrxml before - I've just put in CVS although I don't
have time to check to see what works/doesn't.

Have a look at in CVS.  You'll need XML::SAX on your system.

http://cvs.open-bio.org/

-jason

On Tue, 22 Jun 2004, Fernan Aguero wrote:

> Hi!
>
> I'm seeing an error while trying to parse a .coordset file
> from TIGR. It is my first attempt at using this kind of
> files, so perhaps I'm doing something wrong.
>
> Here's my brief script:
>
> #!/usr/bin/perl -w
>
> use strict;
> use Bio::SeqIO;
>
> my $seqio = Bio::SeqIO->new( -file => $ARGV[0], -format => 'tigr');
>
> Just trying to create a SeqIO object produces the following error:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: [2]Required <ASMBL_ID> missing
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/Root.pm:328
> STACK: Bio::SeqIO::tigr::throw /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/tigr.pm:1338
> STACK: Bio::SeqIO::tigr::_process_assembly /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/tigr.pm:522
> STACK: Bio::SeqIO::tigr::_process /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/tigr.pm:423
> STACK: Bio::SeqIO::tigr::_initialize /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/tigr.pm:90
> STACK: Bio::SeqIO::new /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO.pm:358
> STACK: Bio::SeqIO::new /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO.pm:378
> STACK: ./tigrxml2features.pl:6
> -----------------------------------------------------------
>
>
> The file does contain ASMBL_IDs, or at least that is what I
> believe. These are the first lines of the file
>
> <ASSEMBLY ASMBL_ID = "56" COORDS = "1-2149">
>         <HEADER>
>                 <CLONE_NAME>1047053397923</CLONE_NAME>
>                 <ORGANISM>Trypanosoma cruzi</ORGANISM>
>                 <AUTHOR_LIST CONTACT = "">
>                 </AUTHOR_LIST>
>         </HEADER>
>         <TU FEAT_NAME = "56.t00001" LOCUS = "Tc00.1047053397923.10" PUB_LOCUS =
> "" ALT_LOCUS = "" COM_NAME = "hypothetical protein" PUB_COMMENT = "" COORDS = "1
> 67-586">
>                 <MODEL FEAT_NAME = "56.m00001" COMMENT = "" COORDS = "167-586">
>                         <PROTEIN_SEQ>MKQSSTDGGGKQKGKDSVSSDSMKDAVTDNPGKPTATTIPTSR
> SGDAQEKEGKDDGTDERPTSKKHNSSPETGNTNDALTASENTPQTAETTATTVAKKNDTTIGDSDGSTAVSDTASPLLLL
> FLVVVACAAAAAVVAA*</PROTEIN_SEQ>
>                         <EXON FEAT_NAME = "56.e00001" COORDS = "167-586">
>                                 <CDS FEAT_NAME = "56.c00001" COORDS = "167-586"/
> >
>                         </EXON>
>                 </MODEL>
>         </TU>
> </ASSEMBLY>
>
> I've found a mention of a tigrxml by Jason Stajich that
> was supposed to be different from the SeqIO::tigr by Josh
> Lauricha. But I don't seem to have it in my system
> (bioperl-1.4)
> <http://bioperl.org/pipermail/bioperl-l/2004-January/014491.html>
>
> Thanks in advance,
>
> Fernan
>
> PS: I'm CCing the author of the tigr.pm module, just in
> case.
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu