I am using the method below to load an EMBL file
BufferedReader br = new BufferedReader(new FileReader(emblFile));
stream = SeqIOTools.readEmbl(br);
while (stream.hasNext()){
seq = stream.nextSequence();
}
The problem is that this takes about 10 seconds
I often use the same EMBL files and only want the CDS Features
I feel that there must be a quicker way to do this
As Sequence is Serializable can I save the Sequence to a flat file
and load that instead?
is that possible?
would this be quicker?
would it be more efficient if I removed the features I did not want?
I realise a database might be the way to go - but I dont want to go that way
at the moment.
Simon
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