[Bioperl-l] SeqIO tag/location question

Chris Fields cjfields at illinois.edu
Tue Jul 6 19:10:18 EDT 2010


RefSeq pulls the file from EBI, not from NCBI (IIRC), so maybe there is a difference between the two versions?  Hard to say w/o knowing the exact accession.

chris

On Jul 6, 2010, at 4:54 PM, Tom Keller wrote:

> Greetings,
> A genbank file I am working with has features:
> exon            37167..37302
>                    /gene="SLC12A3"
>                    /gene_synonym="FLJ96318; NCCT; TSC"
>                    /inference="alignment:Splign:1.39.8"
>                    /number=24
>    exon            39189..39256
>                    /gene="SLC12A3"
>                    /gene_synonym="FLJ96318; NCCT; TSC"
>                    /inference="alignment:Splign:1.39.8"
>                    /number=25
>    exon            48058..50644
>                    /gene="SLC12A3"
>                    /gene_synonym="FLJ96318; NCCT; TSC"
>                    /inference="alignment:Splign:1.39.8"
>                    /number=26
> 
> When I parse it using:
> my $db = Bio::DB::RefSeq->new();
> my $seq = $db->get_Seq_by_acc($accession);
> my @features = $seq->get_SeqFeatures;
> for my$feat_obj ( @features ) {
> if ($feat_obj->primary_tag eq 'exon') {
> print "primary tag: ", $feat_obj->primary_tag, " start: ", $feat_obj->start, " end: ",$feat_obj->end, "\n";
> for my $tag ($feat_obj->get_all_tags) {
> for my $value ($feat_obj->get_tag_values($tag)) {
> print "    value: ", $value, "\n";
> }
> }
> }
> }
> 
> I get the following:
> primary tag: exon start: 42167 end: 42302
>   value: SLC12A3
>   value: FLJ96318; NCCT; TSC
>   value: alignment:Splign:1.39.8
>   value: 24
> primary tag: exon start: 44189 end: 44256
>   value: SLC12A3
>   value: FLJ96318; NCCT; TSC
>   value: alignment:Splign:1.39.8
>   value: 25
> primary tag: exon start: 53058 end: 55644
>   value: SLC12A3
>   value: FLJ96318; NCCT; TSC
>   value: alignment:Splign:1.39.8
>   value: 26
> 
> Where does the discrepancy in location (+5000) come from?
> 
> thanks for your help,
> Tom
> MMI DNA Services Core Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
> 4-2442
> kellert at ohsu.edu<mailto:kellert at ohsu.edu>
> RJH (CROET/BasicScience) 6339b
> 
> 
> 
> 
> 
> 
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