Merge pull request #32 from stevenweaver/develop

Quiet mode
veg · Mar 20, 2020 · 2c7e665 · 2c7e665
2 parents 65225d7 + 2e14756
commit 2c7e665
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Showing 4 changed files with 13 additions and 8 deletions.
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 HIVClustering
 -------------
 
-A Python 3 library that makes infers molecular transmission networks from sequence data. A part of [HIV-TRACE](https://academic.oup.com/mbe/article/35/7/1812/4833215), available at http://hivtrace.hyphy.org
+A Python 3 library that makes infers molecular transmission networks from sequence data. A part of [HIV-TRACE](https://academic.oup.com/mbe/article/35/7/1812/4833215), available at http://hivtrace.org
 
 Related projects
 

diff --git a/hivclustering/networkbuild.py b/hivclustering/networkbuild.py
@@ -513,6 +513,7 @@ def build_a_network(extra_arguments = None):
     arguments.add_argument('--before', help='[assumes DATES are available] If provided (as YYYYMMDD) then only allow EDGES that connect nodes with dates at or BEFORE this date', required=False, type = str)
     arguments.add_argument('--import-attributes', dest = 'import_attr', help='Import node attributes from this JSON', required=False, type=argparse.FileType('r'))
     arguments.add_argument('--subcluster-annotation', dest = 'subcluster_annotation', help='As "dist" "field"". Use subcluster annotation for distance "dist" from node attribute "field"  ', required=False, nargs = 2)
+    arguments.add_argument('-q', '--quiet', help='Enable quiet mode',  action='store_true', default=False)
 
 
     if extra_arguments:

diff --git a/scripts/hivnetworkcsv b/scripts/hivnetworkcsv
@@ -232,17 +232,19 @@ def make_hiv_network():
                 for c_id, mapped_id in cluster_map.items():
                     if c_id is None: # singletons
                          if len (mapped_id) > 1 or None not in mapped_id:
-                            report_warning ("Incostistent singletons, nodes previously clustered became unclustered (%s)" % str (mapped_id))
+                            report_warning ("Inconsistent singletons, nodes previously clustered became unclustered (%s)" % str (mapped_id))
                             for old_id in mapped_id:
                                 ensure_key (discrepant_old_clusters, old_id)['disconnected'] = True
 
                     else:
                         if len (mapped_id) == 1:
-                            if None in mapped_id: # new cluster
-                                print ("Cluster %d is a new cluster" % c_id,  file = sys.stderr)
+                            if None in mapped_id :
+                                if not settings().quiet: # new cluster
+                                    print ("Cluster %d is a new cluster" % c_id,  file = sys.stderr)
                             else:
                                 cluster_remap[c_id] = list(mapped_id)[0]
-                                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)
+                                if not settings().quiet:
+                                    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)
@@ -259,7 +261,8 @@ def make_hiv_network():
                                 mapped_id.remove (None)
                                 update_id = list(mapped_id)[0]
                                 cluster_remap[c_id] = update_id
-                                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)
+                                if not settings().quiet:
+                                    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)))
@@ -270,7 +273,8 @@ def make_hiv_network():
                                 mapped_to_existing_clusters.add (c_id)
 
                             else:
-                                print ("Cluster %d MERGES %s" % (c_id, ", ".join ([str(k) for k in list(mapped_id)])), file = sys.stderr)
+                                if not settings().quiet:
+                                    print ("Cluster %d MERGES %s" % (c_id, ", ".join ([str(k) for k in list(mapped_id)])), file = sys.stderr)
                                 if None in mapped_id:
                                     mapped_id.remove (None)
 

diff --git a/setup.py b/setup.py
@@ -8,7 +8,7 @@
 sys.path.insert(0, join(split(abspath(__file__))[0], 'lib'))
 
 setup(name='hivclustering',
-      version="1.6.0",
+      version="1.6.1",
       description='HIV molecular clustering tools',
       author='Sergei Kosakovsky Pond',
       author_email='[email protected]',