My assignment is basically this:
- 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?
- 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?
I used biomart and tried out entrez and embl and they don't work either. What should I do?