[Bioperl-l] Possible Repeat E-Mail

[Fields, Christopher J]

Warren, 

Simple explanation.  The sequence record you are using is a *protein* record; spliced_seq() works on the instance’s sequence (the protein sequence).  

You need the nucleotide sequence associated with this one, so you have to retrieve the nucleotide record associated with it, the one mentioned in the ‘CDS’ feature (the ‘coded_by’ tag) for the file you retrieved:

     CDS             1..1158
                     /gene="KCNH2"
                     /coded_by="NM_001193658.1:14..3490"
                     /db_xref="GeneID:100064000"

and then grab the relevant sequence from that.

chris


On Apr 16, 2014, at 12:37 AM, Warren Gallin <wgallin at ualberta.ca> wrote:

> Jason,
> 
> 	My previous message bounced, presumably because I included an attachment.
> 
> 	On the chance that it did not make it through, here is the relevant test case:
> 
> A script called Test_Script.pl is as follows:
> 
> ____________________________________________________________________
> 
> #!/usr/bin/perl 
> 
> use strict;
> use warnings;
> use DBI;
> use Bio::Seq;
> use Bio::DB::EUtilities;
> use Bio::SeqIO;
> use Bio::Seq;
> use Data::Printer;
> use Bio::DB::GenBank;
> 
> my $gi = 302393575;  #This gi number is for the protein record of a horse ion channel
> my $spliced_cds;
> my $na_seq;
> my %na_vkcnt_id;
> 
> #Create a database handle to GENBANK for retrieving coding sequences
> 
> my $gb_db = Bio::DB::GenBank->new();
> 
> 
> #create a structure for fetching protein records from GENBANK
> 
> my $factory = Bio::DB::EUtilities->new(
>    -eutil   => 'efetch',
>    -db      => 'protein',
>    -rettype => 'gb',
>    -email   => 'wgallin at ualberta.ca',
>    -id      => $gi
> );
> 
> my $holding_file = 'protein_records.gb';
> 
> $factory->get_Response( -file => $holding_file );
> 
> my $seqin = Bio::SeqIO->new(
>    -file   => $holding_file,
>    -format => 'genbank'
> );
> 
> while ( my $seq = $seqin->next_seq ) {
>    my $na_acc_gennt;
>    my $hit_gi = $seq->primary_id;
> 
>    for my $feature_object ( $seq->get_SeqFeatures ) {
> 
>        if ( $feature_object->primary_tag eq "CDS" ) {
>            $spliced_cds = $feature_object->spliced_seq($gb_db);
>            $na_seq      = $spliced_cds->seq;
> 
>        print "UPDATE gennt SET cds = \"$na_seq\" ;\n";
> 		}
>    }
> }
> exit;
> 
> ________________________________________________________
> 
> When I run it I get the following output:
> 
> 
> _________________________________________________________
> 
> warrenglinsmbp2:140414_Update_Flawed_gennt_Entries wgallin$ perl Test_Script.pl
> 
> --------------------- WARNING ---------------------
> MSG: API has changed; please use '-db' or '-nosort' for args. See POD for more details.
> ---------------------------------------------------
> UPDATE gennt SET cds = "MPVRRGHVAPQNTFLDTIIRKFEGQSRKFIIANARVENCAVIYCNDGFCELCGYSRAEVMQRPCTCDFLHGPRTQRRAAAQIAQALLGAEERKVEISFYRKDGSCFLCLVDVVPVKNEDGAVIMFILNFEVVMEKDMVGSPARDTNHRGPPTSWLATGRAKTFRLKLPALLALTARESTVRPGGAGSTGAPGAVVVDVDLTPAAPSSESLALDEVTAMDNHVAGLGPAEERRALVGPGSPPACAPIPHPSPRAHSLNPDASGSSCSLARTRSRESCASVRRASSADDIEAMRTGLPPPPRHASTGAMHPLRSGLLNSTSDSDLVRYRTISKIPQITLNFVDLKGDPFLASPTSDREIIAPKIKERTHNVTEKVTQVLSLGADVLPEYKLQAPRIHRWTILHYSPFKAVWDWLILLLVIYTAVFTPYSAAFLLKETEEGPPATDCGYACQPLAVVDLIVDIMFIVDILINFRTTYVNANEEVVSHPGRIAVHYFKGWFLIDMVAAIPFDLLIFGSGSEELIGLLKTARLLRLVRVARKLDRYSEYGAAVLFLLMCTFALIAHWLACIWYAIGNMEQPHMDSRIGWLHNLGDQIGKPYNSSGLGGPSIKDKYVTALYFTFSSLTSVGFGNVSPNTNSEKIFSICVMLIGSLMYASIFGNVSAIIQRLYSGTARYHTQMLRVREFIRFHQIPNPLRQRLEEYFQHAWSYTNGIDMNAVLKGFPECLQADICLHLNRSLLQHCKPFRGATKGCLRALAMKFKTTHAPPGDTLVHAGDLLTALYFISRGSIEILRGDVVVAILGKNDIFGEPLNLYARPGKSNGDVRALTYCDLHKIHRDDLLEVLDMYPEFSDHFWSSLEITFNLRDTNMIPGSPGSTELEGGFNRQRKRKLSFRRRTDKDPEQPGEVSALGPGRAGAGPSSRGRPGGPWGESPSSGPSSPESSEDEGPGRSSSPLRLVPFSSPRPPGE!
> PPGGEPLIEDCEKSSDTCNPLSGAFSGVSNIFSFWGDSRGRQYQELPRCPAPAPSLLNIPLSSPGRRPRGDVESRLDALQRQLNRLETRLSADMATVLQLLQRQMTLVPPAYSAVTTPGPGPTSTSPLLPVSPIPTLTLDSLSQVSQFMACEELPPGAPELPQDGPTRRLSLPGQLGALTSQPLHRHGSDPGS" ;
> warrenglinsmbp2:140414_Update_Flawed_gennt_Entries wgallin$ 
> 
> 
> ___________________________________________________________
> 
> The problem is that the sequence is being returned as translated CDS rather than the nucleotide sequence of the CDS.
> 
> This happens with every gi number that I have tried.
> 
> I fell like I am missing some subtle BioPerl of wisdom, but I can not figure out what that is.
> 
> Thanks for looking at this.
> 
> Warren Gallin
> 
> 
> 
> 
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