class RecordReceiver:
def __init__(self, handle):
self.handle = handle
def __call__(self, id, rec):
self.handle.write(rec)
# Functor that deals with bad records - prints an error message to HANDLE
class BadRecordReceiver:
def __init__(self, handle):
self.handle = handle
self.badIDs = []
def __call__(self, badID):
self.badIDs.append(badID)
self.handle.write("Bad ID: %s\n" % badID)
# Form pattern for accession strings
accessionPat = prefix + "%%0%dd" % digits
batchSize = 500
for curr in xrange(start, end + 1, batchSize):
# Generate accession strings for this batch
ids = [accessionPat % num for num in range(curr, min(curr + batchSize, end + 1))]
GenBank.download_many(
ids, RecordReceiver(sys.stdout), database="nucleotide", broken_fn=BadRecordReceiver(sys.stderr), faildelay=5.0
)
