[Bioperl-l] Re: Bio ::seqIO ::tigr

[Jay Moore]

Matthieu CONTE reported this:  MSG: [19]Required <AUTHOR_LIST> missing
(See his message below)

I get the same result, and when I looked into tigr.pm, the problem is not actually with the <AUTHOR_LIST> tag, despite the error message, nor I think is the TIGR XML file at fault.  The problem is happening further up the tigr.pm module, in the _process_header method, with the <KEYWORDS> line.  Not sure why (my regex skills are not so hot) but the method does not spot valid <KEYWORDS> lines in the XML.  I found that when I changed the regex in the KEYWORDS line from [^<] to ([^<]*) it would recognise the KEYWORDS tag OK, and progress on, past the <AUTHOR_LIST> as well.  Don't know exactly why, I just copied code from one of the other <HEADER> tags.

So far so good.

For me it bugs out later now - there is no _process_tiling_path method, which there should be.  I reported this one via bugzilla.  To get past this one I chopped the whole <TILING_PATH> object out of the TIGR XML file.

I now get another error later on - 
[79]Required <EXON> Missing.  Still looking at why this one happens.


Matthieu CONTE's original message:

I currently trying to use the Bio ::seqIO ::tigr module.
My objective is to download the whole rice genome form Tigr ( adress 
below)and to integrate it in my BioSQL DB.
For this I am trying to convert the tigr format in swiss format with the 
script below


use Bio::SeqIO;

my $in = Bio::SeqIO->new(-file 
=>'</home/conte/pipeline_orthologues/data/orysa_tigr.txt', -format 
=>'tigr');

my $out = Bio::SeqIO->new(-file => 
'>/home/conte/pipeline_orthologues/data/orysa_swiss.txt' , 
-format=>'swiss');

print $out $_ while <$in>;

I obtain:

------------ EXCEPTION  -------------
MSG: [19]Required <AUTHOR_LIST> missing
STACK Bio::SeqIO::tigr::throw 
/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:1338
STACK Bio::SeqIO::tigr::_process_header 
/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:700
STACK Bio::SeqIO::tigr::_process_assembly 
/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:535
STACK Bio::SeqIO::tigr::_process_tigr 
/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:453
STACK Bio::SeqIO::tigr::_process 
/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:420
STACK Bio::SeqIO::tigr::_initialize 
/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO/tigr.pm:90
STACK Bio::SeqIO::new 
/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:358
STACK Bio::SeqIO::new 
/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/SeqIO.pm:378
STACK toplevel get_bioseq_tigr.pl:8

Could you please tell me if there is a problem with the parser or with the 
input data format of Tigr?

Thanks in advance




Matthieu CONTE
m_conte at hotmail.com

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