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Develop #31

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merged 4 commits into from
Mar 19, 2020
Merged

Develop #31

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5cfd527
Merge pull request #28 from veg/master
stevenweaver Mar 4, 2020
44751de
fix condition where nid is not in cluster_remap
stevenweaver Mar 19, 2020
9156740
Merge branch 'develop' of https://github.com/veg/hivclustering into d…
spond Mar 19, 2020
65225d7
Fixing an issue where existing clusters undergo dramatic changes in -…
spond Mar 19, 2020
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40 changes: 30 additions & 10 deletions scripts/hivnetworkcsv
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Original file line number Diff line number Diff line change
Expand Up @@ -223,9 +223,9 @@ def make_hiv_network():
print ("[WARNING] %s" % message, file = sys.stderr)

def record_multiple_mapping (old_id, new_id):
multi_dict = ensure_key(ensure_key (discrepant_old_clusters, old_id, {}), 'multiple', [])
multi_dict.append (new_id)
multi_dict.extend (list(old_cluster_to_new_cluster[old_id]))
multi_dict = ensure_key(ensure_key (discrepant_old_clusters, old_id, {}), 'multiple', set ())
multi_dict.add (new_id)
multi_dict.update (list(old_cluster_to_new_cluster[old_id]))

old_cluster_to_new_cluster = {}

Expand All @@ -242,7 +242,7 @@ def make_hiv_network():
print ("Cluster %d is a new cluster" % c_id, file = sys.stderr)
else:
cluster_remap[c_id] = list(mapped_id)[0]
print ("Cluster %d matches previous cluster %d" % (c_id, cluster_remap[c_id]), file = sys.stderr)
print ("Cluster %d [%d nodes] matches previous cluster %d [%d nodes]" % (c_id, new_cluster_sizes [c_id], cluster_remap[c_id], old_cluster_sizes[cluster_remap[c_id]]), file = sys.stderr)
cluster_summary_info [cluster_remap[c_id]] = {'type' : 'existing'}
if cluster_remap[c_id] in used_existing_clusters:
record_multiple_mapping (cluster_remap[c_id], c_id)
Expand All @@ -259,7 +259,7 @@ def make_hiv_network():
mapped_id.remove (None)
update_id = list(mapped_id)[0]
cluster_remap[c_id] = update_id
print ("Cluster %d extends previous cluster %d" % (c_id, update_id), file = sys.stderr)
print ("Cluster %d [%d nodes] extends previous cluster %d [%d nodes]" % (c_id, new_cluster_sizes [c_id], update_id, old_cluster_sizes[update_id]), file = sys.stderr)
cluster_summary_info [update_id] = {'type' : 'extended', 'size' : new_cluster_sizes [c_id], 'old_size' : old_cluster_sizes[update_id]}
if cluster_remap[c_id] in used_existing_clusters:
report_warning("Cluster %d from the existing network is mapped to multiple new clusters (nodes %s)" % (update_id, dump_cluster_members (c_id)))
Expand Down Expand Up @@ -296,6 +296,7 @@ def make_hiv_network():




for d_id, d_items in discrepant_old_clusters.items():
'''
Strategies for resolving 'non-canonical clusters'
Expand Down Expand Up @@ -346,17 +347,34 @@ def make_hiv_network():

# update the record for the inheritor (which has shrunk)
cluster_summary_info [d_id] = {'type' : 'extended', 'size' : new_cluster_sizes [inheritor], 'old_size' : old_cluster_sizes[d_id]}



leftovers = set ()
leftovers.update (d_items['multiple'])
# these are NEW clusters that are mapped to THIS old cluster AND some other clusters
# they need to be given a new ID
leftovers.remove (inheritor)
for nid in new_mapping_only_to_old:
if nid != inheritor:
del cluster_remap[nid]
if nid != inheritor:
leftovers.remove (nid)
if nid in cluster_remap:
del cluster_remap[nid]
for n in new_clusters[nid]:
if n.id in old_node_ids:
n.add_attribute ("moved_clusters")

for nid in leftovers:
if nid in cluster_remap:
del cluster_remap[nid]
for n in new_clusters[nid]:
if n.id in old_node_ids:
n.add_attribute ("moved_clusters")

else:
for nid in d_items['multiple']:
del cluster_remap[nid]
for n in new_clusters[nid]:
if nid in cluster_remap:
del cluster_remap[nid]
for n in new_clusters[nid]:
if n.id in old_node_ids:
n.add_attribute ("moved_clusters")

Expand All @@ -368,6 +386,8 @@ def make_hiv_network():
# print (cluster_map[c_id], file = sys.stderr)





for n in network.nodes:
if not n.id in existing_nodes:
Expand Down