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obiclean parallelized

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Celine Mercier
2019-06-20 19:44:04 +02:00
parent 9b4c3537f9
commit 3d9f0352ff
3 changed files with 136 additions and 151 deletions
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9
python/obitools3/commands/clean.pyx
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@ -59,6 +59,13 @@ def addOptions(parser):
default=False,
help="Adds tags for each sequence giving its cluster's head and weight for each sample.")
group.add_argument('--thread-count','-p', # TODO should probably be in a specific option group
action="store", dest="clean:thread-count",
metavar='<THREAD COUNT>',
default=-1,
type=int,
help="Number of threads to use for the computation. Default: the maximum available.")
def run(config):
@ -101,7 +108,7 @@ def run(config):
comments = View.print_config(config, "clean", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
if obi_clean(tobytes(i_dms_name), tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
config['clean']['distance'], config['clean']['ratio'], config['clean']['heads-only'], -1) < 0:
config['clean']['distance'], config['clean']['ratio'], config['clean']['heads-only'], config['clean']['thread-count']) < 0:
raise Exception("Error running obiclean")
# If the input and output DMS are not the same, export result view to output DMS