Question: How do I get Genbank files by using wiki gene ids in bioperl?
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gravatar for anp375
3.2 years ago by
anp375140
anp375140 wrote:

My assignment is basically this:

  1. Take the first fifty gene_IDs from the chr1 and get GenBank reports via a remote blast. Remember the demo video from an earlier lecture?
  2. Return report with all input and output files. 

I'm using Bio::DB::Query::GenBank and Bio::DB::GenBank.

I'm basically sending in the IDs like this:

my $query = Bio::DB::Query::GenBank->new(-ids=>[195052,2981014,11127914]);

And then I make a DB::GenBank object and use the get_stream_by_query method on $query to get a list of sequences. The module description seems to say genbank can recognize wiki gene IDs but I'm getting this error:

MSG: Error from Genbank: Wrong UID 57576

Is there a way to convert it or will I have to do it through biomart?

EDIT:

I used biomart and tried out entrez and embl and they don't work either. What should I do?

genbank bioperl • 1.0k views
ADD COMMENTlink modified 21 months ago by Biostar ♦♦ 20 • written 3.2 years ago by anp375140
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