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

[Heikki Lehvaslaiho]

Matthew,

Under linux you code gives an error: "Not a GLOB reference at ..."

You are trying to mix streams and file handles. Either replace 'new' method 
call in object creation with 'newFh', or replace the while line with:

while ( my $seq = $in->next_seq() ) {
    $out->write_seq($seq);
}

Read more from Bio::SeqIO documentation, e.g:
	http://doc.bioperl.org/releases/bioperl-1.4/Bio/SeqIO.html

Yours,
		-Heikki


On Tuesday 27 Jan 2004 10:50, matthieu CONTE wrote:
> 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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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________