corrected filterReads.new.py

cuffdiff2de.py

@@ -101,7 +101,7 @@ def load_cuffdiff(handle):
 def report(files, pfam, annotation, tab, pTh, verbose):
     """ """
     #load pfam annotation
-    geneid2pfam, geneid2annotation = {},{}
+    geneid2pfam, geneid2annotation, geneid2tab = {}, {}, {}
     if pfam:
         geneid2pfam = load_pfam_tblout(pfam)
         sys.stderr.write(" PFAMs for %s entries loaded.\n" % len(geneid2pfam))
@@ -160,7 +160,7 @@ def report(files, pfam, annotation, tab, pTh, verbose):
             lineData.append( "; ".join(annList))
             #add tab annotation
             annList=[]
-            if transid in geneid2tab:
+            if geneid2tab and transid in geneid2tab:
                 annList.append(";".join(geneid2tab[transid]))
             lineData.append( "; ".join(annList))
             #add Arabidopsis annotation

embl2gtf.py

@@ -32,7 +32,7 @@ def _get_unique_id( gene_id,products,i=1 ):
 
   return new_id
 
-def embl2gtf( source='embl2gtf',allowedTypes=set(['gene', 'CDS', 'tRNA', 'tmRNA', 'rRNA', 'ncRNA']) ): #'mRNA', 
+def embl2gtf( source='embl2gtf',allowedTypes=set(['CDS', 'tRNA', 'tmRNA', 'rRNA', 'ncRNA']) ): #'mRNA', 'gene', 
   """
   """
   #make sure no duplicated products
@@ -67,8 +67,9 @@ def embl2gtf( source='embl2gtf',allowedTypes=set(['gene', 'CDS', 'tRNA', 'tmRNA'
 
       #make sure no duplicated entries in GTF  
       if gene_id in products:
-        sys.stderr.write( "Warning: Duplicated entry found: %s\n" % '; '.join( str(f).split('\n') ) )
-        gene_id = transcript_id = _get_unique_id( gene_id,products ) #continue
+        #sys.stderr.write( "Warning: Duplicated entry found: %s\n" % '; '.join( str(f).split('\n') ) )
+        continue
+        #gene_id = transcript_id = _get_unique_id( gene_id,products ) #continue
 
       products.add(gene_id)
 

filterReads.new.py

@@ -454,7 +454,7 @@ def main():
             exit(-2)
 
     ## Check if prefix is endend with '.' or '_'. Otherwise, add '.' at the end
-    if o.prefix != None and not o.prefix[-1] in ['.', '_']:
+    if o.prefix and not o.prefix[-1] in ['.', '_']:
         o.prefix += '.'
 
     ## We pass file descriptors to the main functions