AUTO-TUNE fixes

hivclustering/networkbuild.py

@@ -2,7 +2,6 @@
 
 import csv
 import argparse
-import operator
 import sys
 import datetime
 import time
@@ -11,14 +10,8 @@
 import json
 import hppy as hy
 import re
-from math import log10, floor, sqrt, exp, log
+from math import sqrt, exp, log
 from hivclustering import *
-from functools import partial
-import multiprocessing
-import hppy as hy
-from operator import itemgetter
-
-
 
 run_settings = None
 uds_settings = None
@@ -692,7 +685,9 @@ def network_report (threshold, network, max_clusters = [0]):
                 if len (rec) > 1:
                     suggested_span = max (rec, key = lambda x: x[0])[0] - min (rec, key = lambda x: x[0])[0]
                     mean_diff = sum ([k[1] - profile[i-1][1] for i,k in enumerate(profile[1:])]) / (len (profile)-1)
-                    if (suggested_span / mean_diff < log (len (profile))):
+                    if mean_diff == 0.0:
+                        pass
+                    elif (suggested_span / mean_diff < log (len (profile))):
                         run_settings.threshold = rec[0][0]
 
             if run_settings.threshold is None:

scripts/hivnetworkannotate

@@ -71,6 +71,8 @@ import_settings = arguments.parse_args()
 
 results_json = json.load (import_settings.network)
 
+root_trace_results = False
+
 if('trace_results' in results_json.keys()):
     root_trace_results = True
 
@@ -143,6 +145,7 @@ else: # TSV import
             raise "Invalid field to index on (%s)" % import_settings.index
 
     to_import = {}
+
     try:
         for line in csv_reader:
             to_import [line[index_on]] = {}
@@ -172,7 +175,7 @@ for n, values in to_import.items():
         for k, val in values.items():
             if k in field_transformations:
                 store_this = field_transformations[k] (val)
-                if store_this is not None:
+                if store_this is not None and node_dict is not None:
                     node_dict[field_names[k]] = store_this
                     if node_id in uninjected_set[field_names[k]]:
                         uninjected_set[field_names[k]].remove (node_id)
@@ -197,7 +200,7 @@ if inject_missing_value:
 if import_settings.inplace and import_settings.network is not sys.stdin:
     import_settings.output = open (import_settings.network.name, "w")
 
-if 'Settings' in network_json and 'compact_json' in network_json['Settings']:
+if 'Settings' in network_json and 'compact_json' in network_json['Settings'] and network_json['Settings']['compact_json']:
      ht_compress_network_json (network_json)
 
 # Return with trace_results key
@@ -208,4 +211,4 @@ else:
     to_return = network_json
 
 
-json.dump(to_return, import_settings.output, separators=(',', ':'))
+json.dump(to_return, import_settings.output, indent=2, separators=(',', ':'))

scripts/hivnetworkcsv

@@ -101,7 +101,8 @@ def make_hiv_network():
 
 
         cluster_summary_info = None
-
+        prior_network_subclusters = None
+
         if settings().prior is not None:
             try:
                 existing_nodes      = {} # node ID -> cluster ID
@@ -617,5 +618,6 @@ def make_hiv_network():
     return network
 
 if __name__ == '__main__':
+    __spec__ = None
     make_hiv_network()