[Bioperl-l] (no subject)

[Brian Osborne]

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
>> -------------------------------------------------------------
>> 
>> 
>> _______________________________________________
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>> 
> 
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