Create orthoxml2rootHOGidLevel.py

Author: sinamajidian

utils/orthoxml2rootHOGidLevel.py

@@ -0,0 +1,42 @@
+
+import sys
+import logging
+import pyham
+
+
+"""
+To run
+python orthoxml2rootHOGidLevel.py fastoma_out
+fastoma_out: where species_tree_checked.nwk and FastOMA_HOGs.orthoxml are located.
+
+output: 
+a two-column tsv file, HOGid taxid
+
+"""
+
+
+fastoma_out=sys.argv[1] 
+
+treeFile=fastoma_out+'/species_tree_checked.nwk'
+orthoxmlFile=fastoma_out+'/FastOMA_HOGs.orthoxml'
+
+
+logging.basicConfig(format='%(asctime)s %(levelname)-8s %(message)s', level=logging.INFO, datefmt='%Y-%m-%d %H:%M:%S')
+logger = logging.getLogger("hog")
+logger.setLevel(logging.INFO)
+
+ham_analysis = pyham.Ham(treeFile, orthoxmlFile, use_internal_name=True)
+rootHOG_dic=ham_analysis.get_dict_top_level_hogs()
+HOGid_level_list=[]
+for HOGid, HOG in rootHOG_dic.items():
+    level=HOG.__dict__['_properties']['TaxRange']
+    HOGid_level_list.append((HOGid,level))
+print('We found ' +str(len(HOGid_level_list))+ ' rootHOGs.')
+
+output_f = open('FastOMA_HOGs.level.tsv','w')
+output_f.write('##rootHOGid'+'\t'+'TaxRange'+'\n')
+for HOGid,level  in HOGid_level_list :
+    output_f.write(HOGid+'\t'+level+'\n')
+output_f.close()
+
+print('RootHOGs level info is written in FastOMA_HOGs.level.tsv')