parsing a fasta file using a generator ( python )

Question

I am trying to parse a large fasta file and I am encountering out of memory errors. Some suggestions to improve the data handling would be appreciated. Currently the program

Answer 1

Without having a great understanding of what you are doing, I would have written the code like this:

def readFastaEntry( fp ):
    name = ""
    while True:
        line = name or f.readline()
        if not line:
            break
        seq = []
        while True:
            name = f.readline()
            if not name or name.startswith(">"):
                break
            else:
                seq.append(name)
        yield (line, "".join(seq))

This gathers up the data after a starting line up to the next starting line. Making seq an array means that you minimize the string joining until the last possible moment. Yielding a tuple makes more sense than a list.