In the fasta_alignment_to_subnet() function, there is a
copy.deepcopy(true_start)
that according to profiling is taking way too long. A suggested solution is using
g = cPickle.loads(cPickle.dumps(a, -1))
as suggested here:
https://stackoverflow.com/questions/24756712/deepcopy-is-extremely-slow
Will try this first, but otherwise the whole fasta_alignment_to_subnet() function could do with improvement.
jambler24
commented
6 years ago
In the fasta_alignment_to_subnet() function, there is a
copy.deepcopy(true_start)that according to profiling is taking way too long. A suggested solution is usingg = cPickle.loads(cPickle.dumps(a, -1))as suggested here: https://stackoverflow.com/questions/24756712/deepcopy-is-extremely-slow Will try this first, but otherwise the whole fasta_alignment_to_subnet() function could do with improvement.