[Bioperl-l] Re: Error parsing TIGR xml

[Josh Lauricha]

The TIGR parser in bioperl 1.4 doesn't parse the coordset files, it  
parses the full-fledged
TIGR xml releases. Jason wrote an unpublished parser for the coordsets,  
which while
similar files are different enough to really need a different parser.

One thing, is that IIRC, the coordsets do not contain any sequence  
data, so you'll need to
also lookup the actual sequence.

On Jun 22, 2004, at 10:21 AM, 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
> SGDAQEKEGKDDGTDERPTSKKHNSSPETGNTNDALTASENTPQTAETTATTVAKKNDTTIGDSDGSTAVS 
> DTASPLLLL
> 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.
>
> -- 
> F e r n a n   A g u e r o
> http://genoma.unsam.edu.ar/~fernan
>
Josh Lauricha
laurichj at bioinfo.ucr.edu
OpenPGP: 5A0D 92D3 D093 79DE F724 1137 6DF1 B5EB D9CE AAA8

Josh Lauricha
laurichj at bioinfo.ucr.edu
OpenPGP: 5A0D 92D3 D093 79DE F724 1137 6DF1 B5EB D9CE AAA8
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