v0.7.4

- Added new column proteome_with_domain_fraction
DRL · Dec 18, 2016 · 0117fd5 · 0117fd5
1 parent 7f32892
commit 0117fd5
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/kinfin.py b/kinfin.py
@@ -729,6 +729,7 @@ def get_header_line(self, filetype, attribute):
             cluster_metrics_domains_detailed_header.append("domain_description")
             cluster_metrics_domains_detailed_header.append("protein_count")
             cluster_metrics_domains_detailed_header.append("protein_count_with_domain")
+            cluster_metrics_domains_detailed_header.append("proteomes_with_domain_fraction")
             cluster_metrics_domains_detailed_header.append("proteomes_with_domain")
             cluster_metrics_domains_detailed_header.append("proteomes_without_domain")
             return "\t".join(cluster_metrics_domains_detailed_header)
@@ -957,16 +958,19 @@ def write_cluster_metrics(self):
                                             cluster_metrics_domains_detailed_output_line.append("N/A")
                                     cluster_metrics_domains_detailed_output_line.append(clusterObj.protein_count)
                                     protein_with_domain_count_by_proteome_id = {}
+                                    proteome_count_with_domain = 0
                                     protein_without_domain_count_by_proteome_id = {}
                                     for proteome_id, protein_ids in clusterObj.protein_ids_by_proteome_id.items():
                                         for protein_id in protein_ids:
                                             if domain_source in proteinCollection.proteinObjs_by_protein_id[protein_id].domain_counter_by_domain_source and domain_id in proteinCollection.proteinObjs_by_protein_id[protein_id].domain_counter_by_domain_source[domain_source]:
                                                 protein_with_domain_count_by_proteome_id[proteome_id] = protein_with_domain_count_by_proteome_id.get(proteome_id, 0) + 1
+                                                proteome_count_with_domain += 1
                                             else:
                                                 protein_without_domain_count_by_proteome_id[proteome_id] = protein_without_domain_count_by_proteome_id.get(proteome_id, 0) + 1
                                     proteomes_with_domain_count_string = ",".join(sorted(["%s:%s/%s" % (proteome_id, count, len(clusterObj.protein_ids_by_proteome_id[proteome_id])) for proteome_id, count in protein_with_domain_count_by_proteome_id.items()]))
                                     proteomes_without_domain_count_string = ",".join(sorted(["%s:%s/%s" % (proteome_id, count, len(clusterObj.protein_ids_by_proteome_id[proteome_id])) for proteome_id, count in protein_without_domain_count_by_proteome_id.items()]))
                                     cluster_metrics_domains_detailed_output_line.append(sum(protein_with_domain_count_by_proteome_id.values()))
+                                    cluster_metrics_domains_detailed_output_line.append("{0:.3f}".format(proteome_count_with_domain/clusterObj.proteome_count))
                                     cluster_metrics_domains_detailed_output_line.append(proteomes_with_domain_count_string)
                                     cluster_metrics_domains_detailed_output_line.append(proteomes_without_domain_count_string)
                                     cluster_metrics_domains_detailed_output_by_domain_source[domain_source].append("\t".join([str(field) for field in cluster_metrics_domains_detailed_output_line]))
@@ -2119,7 +2123,7 @@ def welcome_screen():
     " % (__version__)
     print screen
 if __name__ == "__main__":
-    __version__ = "0.7.3"
+    __version__ = "0.7.4"
     args = docopt(__doc__)
     # Sanitise input
     welcome_screen()