Debug with source from prod.

workflows/rnaseqdenovo/__init__.py

@@ -605,7 +605,7 @@ class RNAseqDenovo (ApplicationWithoutReferenceGenome):
         dna = self.add_biomart_load(DNA, [self.assembly["file"]])
 
         # load the go table
-        if self.go:
+        if self.go != None:
             go_convert = self.add_component( "GO2topGO", [self.go], component_prefix="GOUser" )
             go = self.add_biomart_load(GO, [self.go], "Gene Ontology",
                                    "GO",
@@ -618,7 +618,7 @@ class RNAseqDenovo (ApplicationWithoutReferenceGenome):
                                    None)
 
         # load the keyword table
-        if self.keyword:
+        if self.keyword != None:
             kw = self.add_biomart_load(Keyword, [self.keyword])
 
         # load the variant tables

workflows/rnaseqdenovo/components/renamerules.py

@@ -45,7 +45,7 @@ def renames_with_annot( prefix, inputs, rename_file):
                 clean_gene = ""
                 gene_name = record.attributesToStr("gene")
                 for char in gene_name:
-                    if char.isalnum() or char in ['.', ':', '^', '*', '$', '@', '!', '+', '_', '?', '-', '|']: # GFF3 seqid specifications
+                    if char.isalnum() or char in ['.', '^', '*', '$', '@', '!', '+', '_', '?', '-', '|']: # GFF3 seqid specifications
                         clean_gene += char
                 dict_contig_id_gene[record.seq_id] = clean_gene
                 if dict_gene_contig_id.has_key(clean_gene) :