Merge pull request #53 from FOI-Bioinformatics/name_bug_issue51_fix

Name bug issue51 fix

flextaxd/modules/NewickTree.py

@@ -15,6 +15,11 @@
 import logging
 logger = logging.getLogger(__name__)
 
+try:
+	import inquirer
+except:
+	Raise(ImportError("The package inquirer is required for flextaxd visualisation"))
+
 
 __version__ = "0.0.1"
 __author__ = "David Sundell"
@@ -340,7 +345,6 @@ def double_vis_path(self,duplicates,taxid,nodes):
 		            ),
 		]
 		selected = inquirer.prompt(questions)["parent"]
-		import random
 		n = random.randint(10000000,10100000)
 		if selected != default:
 			children[0],children[1] = children[1],children[0]

flextaxd/modules/ProcessDirectory.py

@@ -164,7 +164,7 @@ def walk_directory(self,folder_path):
 		logger.info("Process genome path ({path})".format(path=folder_path))
 		for root, dirs, files in os.walk(folder_path,followlinks=True):
 			for file in files:
-				fname = file.strip(".gz") ## remove gz if present
+				fname = file.rstrip(".gz") ## remove gz if present
 				if fname.endswith(tuple(self.ext)):
 					if count % 1000 == 0:
 						print("Processed {count} genomes".format(count=count), end="\r")

flextaxd/modules/ReadTaxonomyQIIME.py

@@ -36,7 +36,7 @@ def __init__(self, taxonomy_file=False, names_dmp=False, database=False, verbose
 		}
 		self.set_qiime(True)
 		### Add root name these manual nodes are required when parsing the GTDB database!
-		rootid = self.add_node("root")  ## Allways set in ReadTaxonomy
+		rootid = self.root ## Allways set in ReadTaxonomy
 		coid = self.add_node("cellular organisms")
 		bac_id = self.add_node("Bacteria")
 		Euk_id = self.add_node("Eukaryota")
@@ -48,7 +48,7 @@ def __init__(self, taxonomy_file=False, names_dmp=False, database=False, verbose
 		self.add_rank("n",qiime=True)
 		self.add_rank("sk",qiime=True)
 		## Add basic links
-		self.add_link(child=rootid, parent=rootid,rank="n")
+		#self.add_link(child=rootid, parent=rootid,rank="n") ## Already done in ReadTaxonomy
 		self.add_link(child=coid, parent=rootid,rank="n")
 		self.add_link(child=bac_id, parent=coid,rank="sk")
 		self.add_link(child=Euk_id, parent=coid,rank="sk")