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jhannah@klab:~/src/sandbox/Meteorswarm$ cat medicago_chr0_20080103.xml | perl j.pl tigrxml
--------------------- WARNING ---------------------
MSG: Unknown element TIGR, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element ASMBL_ID, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element COORDSET, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element END5, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element END3, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element SEQ_LAST_TOUCHED, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element DATE, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element GB_ACCESSION, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element SEQ_GROUP, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element GENE_LIST, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element PROTEIN_CODING, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element FEAT_NAME, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element DATE, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element GENE_INFO, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element LOCUS, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element COM_NAME, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element IS_PSEUDOGENE, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element DATE, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element COORDSET, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element END5, ignored
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Unknown element END3, ignored
---------------------------------------------------
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: start is undefined
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/jhannah/src/bioperl-live/Bio/Root/Root.pm:368
STACK: Bio::RangeI::contains /home/jhannah/src/bioperl-live/Bio/RangeI.pm:255
STACK: Bio::SeqFeature::Generic::add_SeqFeature /home/jhannah/src/bioperl-live/Bio/SeqFeature/Generic.pm:783
STACK: Bio::SeqIO::tigrxml::start_element /home/jhannah/src/bioperl-live/Bio/SeqIO/tigrxml.pm:206
STACK: try{} block /usr/share/perl5/XML/SAX/Base.pm:292
STACK: XML::SAX::Base::start_element /usr/share/perl5/XML/SAX/Base.pm:266
STACK: XML::SAX::PurePerl::element /usr/share/perl5/XML/SAX/PurePerl.pm:241
STACK: XML::SAX::PurePerl::content /usr/share/perl5/XML/SAX/PurePerl.pm:294
STACK: XML::SAX::PurePerl::element /usr/share/perl5/XML/SAX/PurePerl.pm:246
STACK: XML::SAX::PurePerl::content /usr/share/perl5/XML/SAX/PurePerl.pm:294
STACK: XML::SAX::PurePerl::element /usr/share/perl5/XML/SAX/PurePerl.pm:246
STACK: XML::SAX::PurePerl::content /usr/share/perl5/XML/SAX/PurePerl.pm:294
STACK: XML::SAX::PurePerl::element /usr/share/perl5/XML/SAX/PurePerl.pm:246
STACK: XML::SAX::PurePerl::content /usr/share/perl5/XML/SAX/PurePerl.pm:294
STACK: XML::SAX::PurePerl::element /usr/share/perl5/XML/SAX/PurePerl.pm:246
STACK: XML::SAX::PurePerl::content /usr/share/perl5/XML/SAX/PurePerl.pm:294
STACK: XML::SAX::PurePerl::element /usr/share/perl5/XML/SAX/PurePerl.pm:246
STACK: XML::SAX::PurePerl::document /usr/share/perl5/XML/SAX/PurePerl.pm:131
STACK: XML::SAX::PurePerl::_parse /usr/share/perl5/XML/SAX/PurePerl.pm:103
STACK: XML::SAX::PurePerl::_parse_bytestream /usr/share/perl5/XML/SAX/PurePerl.pm:57
STACK: XML::SAX::Base::parse /usr/share/perl5/XML/SAX/Base.pm:2602
STACK: XML::SAX::Base::parse_file /usr/share/perl5/XML/SAX/Base.pm:2631
STACK: Bio::SeqIO::tigrxml::next_seq /home/jhannah/src/bioperl-live/Bio/SeqIO/tigrxml.pm:116
STACK: j.pl:10
-----------------------------------------------------------
jhannah@klab:~/src/sandbox/Meteorswarm$
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