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fix: pass threads to mash sketch #238

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fix: pass threads to mash sketch #238

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6 changes: 3 additions & 3 deletions drep/d_cluster/compare_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,12 +29,12 @@ def __init__(self, locations, number, sketch_folder, genome_names, no_create=Fal
if not os.path.exists(self.chunk_folder):
os.makedirs(self.chunk_folder)

def gen_sketch_cmds(self, mash_exe, MASH_s):
def gen_sketch_cmds(self, mash_exe, MASH_s, p):
cmds = []
for location, name in zip(self.genome_locations, self.genome_names):
file = os.path.join(self.chunk_folder, name)
if not os.path.isfile(file + '.msh'):
cmd = [mash_exe, 'sketch', location, '-s', str(MASH_s), '-o',
cmd = [mash_exe, 'sketch', location, '-p', str(p), '-s', str(MASH_s), '-o',
file]
cmds.append(cmd)
return cmds
Expand Down Expand Up @@ -170,7 +170,7 @@ def run_mash_on_genome_chunks(genome_chunks, mash_exe, sketch_folder, MASH_folde
# Step 1) Create Mash sketches
cmds = []
for GC in genome_chunks:
cmds += GC.gen_sketch_cmds(mash_exe, MASH_s)
cmds += GC.gen_sketch_cmds(mash_exe, MASH_s, p)
if (not dry) & (len(cmds) > 0):
drep.thread_cmds(cmds, logdir=logdir, t=int(p))

Expand Down