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Feature/kmeans manyparts #114

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Feature/kmeans manyparts #114

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19072fe
update so k-means can use ML tree...
roblanf Jul 25, 2016
a4a5718
make RAxML fall back on standard raxml with one CPU
roblanf Jul 25, 2016
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17 changes: 14 additions & 3 deletions partfinder/analysis_method.py
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Original file line number Diff line number Diff line change
Expand Up @@ -762,14 +762,25 @@ def setup(self):
if the_config.min_subset_size == False:
the_config.min_subset_size = 100

partnum = len(the_config.user_subsets)
the_config.progress.begin(1, 1)

# we start by putting all the partitions together.
# we do this because I don't like the idea of starting with user-defined
# partitions and trying to split them one by one. But I don't know if
# this is really defensible. Still, we have to start somewhere.
# but doing it this way allows us to first estimate an ML tree with
# all subsets separate, which is generally useful.
user_partnum = len(the_config.user_subsets)

# Start with the most partitioned scheme
start_description = range(partnum)
start_description = [0]*user_partnum
start_scheme = scheme.create_scheme(
the_config, "start_scheme", start_description)

partnum = 1
the_config.progress.begin(1, 1)

print start_scheme.subsets

if len(start_scheme.subsets)>1:
log.error("The k-means algorithm is designed to analyse \
the entire alignment at once. To use it, please define a \
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6 changes: 6 additions & 0 deletions partfinder/raxml.py
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Expand Up @@ -71,6 +71,11 @@ def run_raxml(command):

def run_raxml_pthreads(command, cpus):
global _raxml_pthreads_binary

# fall back on standard raxml if the number of cpus is 1
if(cpus==1):
run_raxml(commmand)

if _raxml_pthreads_binary is None:
_raxml_pthreads_binary = util.find_program(_binary_name_pthreads)
command = " ".join([command, "-T", str(cpus), " "])
Expand Down Expand Up @@ -115,6 +120,7 @@ def make_ml_topology(alignment_path, datatype, cmdline_extras, scheme, cpus):
command = ''.join([command, " -w '%s'" % os.path.abspath(aln_dir)])

run_raxml_pthreads(command, cpus)

alndir, aln = os.path.split(alignment_path)

fast_tree_path = os.path.join(alndir, "RAxML_fastTree.fastTREE")
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