Add refresh option for build_fragment_fasta #22
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If refresh is True, force rebuilding the blastdb, this refresh parameter is passed down from build_db in the build_db code. So when build_db is called with refresh=True, fragment blastdb will be rebuilt, which should be the correct behavior.
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Hi @myw, could you take a look at this? I need this functionality to rebuild a blastdb for a problematic genome from the ground up (rebuilding blastdb for all the fragments). I think this would be a generally useful feature. This should not slow down the normal operations in Edge that calls the build_db since most of the call came from check_and_build_genome_db which defaults with refresh=False and that's mostly what happens. Having this refresh=True option for building fragments will enable me to directly call build_genome_db with refresh=True to rebuilding the blastdb for all the fragments. Thanks! |
myw
suggested changes
Feb 20, 2018
src/edge/blastdb.py
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| fn = fragment_fasta_fn(fragment) | ||
| make_required_dirs(fn) | ||
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| if not os.path.isfile(fn): # have not built this fasta | ||
| if not os.path.isfile(fn) or refresh is True: # have not built this fasta |
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no need to say is True; fine to just evaluate it as boolean: if … or refresh:
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If refresh is True, force rebuilding the blastdb, this refresh
parameter is passed down from build_db in the build_db code. So when
build_db is called with refresh=True, fragment blastdb will be rebuilt,
which should be the correct behavior.