CodeMassage

- Added Try/Except to Nodes.dmp/Names.dmp parsing
- Made error message more fitting

Author: Dom Laetsch

lib/BtIO.py

@@ -251,26 +251,32 @@ def getNodesDB(**kwargs):
         print BtLog.status_d['3'] % (kwargs['nodes'], kwargs['names'])
         nodesDB = {}
         nodes_count = 0
-        with open(kwargs['nodes']) as fh:
-            for line in fh:
-                nodes_col = line.split("\t")
-                node = {}
-                node_id = nodes_col[0]
-                node['parent'] = nodes_col[2]
-                node['rank'] = nodes_col[4]
-                nodesDB[node_id] = node
-                nodes_count += 1
-        with open(kwargs['names']) as fh:
-            for line in fh:
-                names_col = line.split("\t")
-                if names_col[6] == "scientific name":
-                   nodesDB[names_col[0]]['name'] = names_col[2]
-        nodesDB_f = kwargs['nodesDB']
-        nodesDB['nodes_count'] = nodes_count
+        try:
+            with open(kwargs['nodes']) as fh:
+                for line in fh:
+                    nodes_col = line.split("\t")
+                    node = {}
+                    node_id = nodes_col[0]
+                    node['parent'] = nodes_col[2]
+                    node['rank'] = nodes_col[4]
+                    nodesDB[node_id] = node
+                    nodes_count += 1
+            with open(kwargs['names']) as fh:
+                for line in fh:
+                    names_col = line.split("\t")
+                    if names_col[6] == "scientific name":
+                       nodesDB[names_col[0]]['name'] = names_col[2]
+            nodesDB_f = kwargs['nodesDB']
+            nodesDB['nodes_count'] = nodes_count
+        except:
+            BtLog.error('3')
     elif (kwargs['nodesDB']):
-        print BtLog.status_d['4'] % (kwargs['nodesDB'])
-        nodesDB = readNodesDB(kwargs['nodesDB'])
-        nodesDB_f = kwargs['nodesDB']
+        try:
+            print BtLog.status_d['4'] % (kwargs['nodesDB'])
+            nodesDB = readNodesDB(kwargs['nodesDB'])
+            nodesDB_f = kwargs['nodesDB']
+        except:
+            BtLog.error('3')
     else:
         BtLog.error('3')
     return nodesDB, nodesDB_f

lib/BtLog.py

@@ -4,7 +4,7 @@
 """
 File        : BtLog.py
 Version     : 0.1
-Author      : Dominik R. Laetsch, dominik.laetsch at gmail dot com 
+Author      : Dominik R. Laetsch, dominik.laetsch at gmail dot com
 Bugs        : ?
 To do       : ?
 """
@@ -34,7 +34,7 @@ def progress(iteration, steps, max_value):
     '0' : '[ERROR:0]\t: File %s does not exist.',
     '1' : '[ERROR:1]\t: Please provide coverage information.',
     '2' : '[ERROR:2]\t: Assembly type is not valid (%s).',
-    '3' : '[ERROR:3]\t: nodesDB ("--db") or names.dmp/nodes.dmp ("--nodes", "--names") not specified.',
+    '3' : '[ERROR:3]\t: nodesDB ("--db") or names.dmp/nodes.dmp ("--nodes", "--names") could not be read.',
     '4' : '[ERROR:4]\t: BlobDB.parseFasta() - no sequences found. Check FASTA file.',
     '5' : '[ERROR:5]\t: Sequence header %s is not unique.',
     '6' : '[ERROR:6]\t: BlobDB.readBam() - sequence header %s in %s was not in FASTA.',
@@ -61,7 +61,7 @@ def progress(iteration, steps, max_value):
 }
 
 warn_d = {
-    '0' : '[WARN]\t: No tax files specified.', 
+    '0' : '[WARN]\t: No tax files specified.',
     '1' : '[WARN]\t: %s not in colour file %s ...',
     '2' : '[WARN]\t: %s in file %s is not part of the assembly',
     '3' : '[WARN]\t: samtools flagstat reported %s mapped reads, %s mapped reads were parsed',
@@ -87,5 +87,5 @@ def progress(iteration, steps, max_value):
     '0' : '\t[INFO]\t: %s : sequences = %s, span = %s MB, N50 = %s nt'
     }
 
-if __name__ == "__main__": 
-    pass
+if __name__ == "__main__":
+    pass