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6 hours ago by

I am trying the examples described here biopython.org/wiki/BioSQL

First I create the database orchids and then I try to use lookup using the code provided

from BioSQL import BioSeqDatabase

server = BioSeqDatabase.open_database(
driver="mysql.connector",
user="root",
passwd="your-password",
host="localhost",
db="bioseqdb",
)
db = server["orchids"]
for identifier in ["6273291", "6273290", "6273289"]:
    seq_record = db.lookup(gi=identifier)
    printseq_record.id, seq_record.description[:50] + "...")
    print("Sequence length %i," % len(seq_record.seq))

But it seems that the gi's are the id's such as 'AF191665', 'AF191664' and 'AF191663'. Is this the only way to lookup BioSQL entries?



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