[Bioperl-l] Re: (no subject)

[Olena Morozova]

Thank you very much for your reply, Brian.

The script works when I write out the actual ID like this:
my $seq = $inx->fetch('GSTENP00038948001')
However, it does not work when I try to fetch the sequence by the same
ID written in a file (I tried just putting this one ID in the file)...



On 12/6/05, Brian Osborne <osborne1 at optonline.net> wrote:
> Olena,
>
> This is _probably_ the problem described in the FAQ:
>
> http://bioperl.org/Core/Latest/faq.html#Q2.5
>
>
> Brian O.
>
>
> On 12/6/05 12:13 PM, "Olena Morozova" <olenka.m at gmail.com> wrote:
>
> > Hi,
> >
> > I am trying to extract sequences from a fasta file using the script
> > below (the fasta file has been indexed). I keep getting the message:
> > failure to provide a valid PrimarySeqI object. Why is this?
> >
> > Thanks a lot for all your help!!
> > Olena
> >
> >
> > #! /usr/bin/perl -w
> >
> >     use Bio::Index::Fasta;
> >     use strict;
> >
> >     my $Index_File_Name = "c:/perl/known.fa";
> >     my $inx = Bio::Index::Fasta->new('-filename' => $Index_File_Name);
> >     my $out = Bio::SeqIO->new('-format' => 'Fasta','-fh' => \*STDOUT);
> >
> >     foreach my $id ('puffer_tf_id1.txt') {
> >         my $seq = $inx->fetch($id); # Returns Bio::Seq object
> > $out->write_seq($seq);
> >     }
> > On 12/6/05, Hilmar Lapp <hlapp at gmx.net> wrote:
> >> Good point. No there is no such module, i.e., one that would implement
> >> RandomAccessI for BioSQL. Shouldn't be hard to write though; would you
> >> be inclined to volunteer?
> >>
> >> -hilmar
> >>
> >> On Dec 5, 2005, at 10:27 AM, Razvan Sultana wrote:
> >>
> >>> Hi !
> >>> I have a question regarding the bioperl-db implementation in Oracle.
> >>> I have created a BioSQL schema in Oracle and populated with the latest
> >>> version of Genbank.
> >>> I used the "bleeding edge" version of bioperl, bioperl-db and
> >>> bioperl-schema from the CVS repository.
> >>>
> >>> When I try to extract the spliced sequences of the CDS features of
> >>> entries that have remote locations (e.g., for AF327267:
> >>> join(4..190,AF327268.1:89..275,AF327268.1:780..930,
> >>>                     AF327268.1:1049..1196,AF327269.1:63..229,
> >>>                     AF327269.1:522..659,AF327269.1:784..917,
> >>>                     AF327269.1:1461..1582,AF327270.1:100..173,
> >>>                     AF327270.1:349..417)
> >>> the appended  code complains that it
> >>> Can't locate object method "get_Seq_by_acc" via package
> >>> "Bio::DB::BioSQL::DBAdaptor"
> >>> and rightly so, because the above object doesn't implement the
> >>> Bio::DB::RandomAccessI interface.
> >>> If I omit $db from the spliced_seq() method call, I obviously get the
> >>> message:
> >>> MSG: cannot get remote location for AF327268.1 without a valid
> >>> Bio::DB::RandomAccessI database handle (like Bio::DB::GenBank)
> >>>
> >>> My question is: is there an object to the BioSQL schema that
> >>> implements Bio::DB::RandomAccessI ?
> >>> If there is, how do I get a handle to it?
> >>> If there isn't, I would be willing to help implementing it.
> >>>
> >>> Thank you,
> >>> Razvan Sultana
> >>>
> >>> #!/usr/local/bin/perl
> >>> use strict;
> >>> use Bio::DB::BioDB;
> >>> use Bio::Seq::RichSeq;
> >>> use Bio::DB::Query::BioQuery;
> >>> use Getopt::Long;
> >>>
> >>> my $host = 'kevin';
> >>> my $dbuser = 'biosql';
> >>> my $dbpass;
> >>> my $dbname = 'biocompd';
> >>> my $driver = 'Oracle';
> >>> my $acc;
> >>> my $biodbname = 'genbank';
> >>>
> >>> &GetOptions( 'host=s' => \$host,
> >>>             'driver=s' => \$driver,
> >>>         'dbuser=s' => \$dbuser,
> >>>         'dbpass=s' => \$dbpass,
> >>>         'dbname=s' => \$dbname,
> >>>         'accession=s' => \$acc);
> >>> $acc = 'AF327270' unless $acc;
> >>>
> >>> my $db = Bio::DB::BioDB->new(-database => "biosql",
> >>>                 -host     => $host,
> >>>                 -dbname   => $dbname,
> >>>                 -driver   => $driver,
> >>>                 -user     => $dbuser,
> >>>                 -pass     => $dbpass,
> >>>                 );
> >>>
> >>> my $seqadaptor = $db->get_object_adaptor('Bio::SeqI');
> >>> my $query = Bio::DB::Query::BioQuery->new(-datacollections =>
> >>> ['Bio::PrimarySeqI e',
> >>>
> >>> 'BioNamespace=>Bio::PrimarySeqI db'],
> >>>                                          -where =>
> >>> ["e.accession_number = '$acc'",
> >>>                                                     "db.namespace=
> >>> '$biodbname'"]);
> >>> my $seq_object = Bio::Seq::RichSeq->new();
> >>> my $query_result = $seqadaptor->find_by_query($query);
> >>>
> >>> while ($seq_object = $query_result->next_object()) {
> >>>  for my $feature ($seq_object->get_SeqFeatures()) {
> >>>    my $full_sequence = $seq_object->seq();
> >>>    my $cds_seq = $feature->spliced_seq($db)->seq() if
> >>> ($feature->primary_tag() eq 'CDS');
> >>>  }
> >>> }
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at portal.open-bio.org
> >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >> --
> >> -------------------------------------------------------------
> >> Hilmar Lapp                            email: lapp at gnf.org
> >> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> >> -------------------------------------------------------------
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at portal.open-bio.org
> >> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
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