[gt-users] method to either delete a child from a FeatureNode, or to update its type

[La Rota, Mauricio]

Hi Sascha and Gordon,

Is there a way to update the type of an already existing child feature? What about to remove it and recreate a correct one?

 I  am trying to correct the type for the wrongly labeled UTRs in the GFF files I am working with (I sent two sample GFF files yesterday in the thread "A series of questions regarding GenomeTools C and its Python interface")  and since I don't see a way to modify (or have access to) a FeatureNode's type with something like FeatureNode.setType() I was instead trying to remove the child node (with fn.__del__) and recreating a new one in its place.

Of the two choices, it might be cleaner just o update the type.  The sample GFF contains some gene models for which the UTRs labels are reversed (5' should be 3' or viceversa).

Please see my python function below where I was trying to take a pointer to the current child_feature, checking it and returning the same one if nothing needed updating or destroying it and recreating a new one.  See line annotated with "****"

Thanks,

Mauricio.

I would call it like this:

haveSeenCDS = False
fni = FeatureNodeIteratorDirect(feature)
tfn  = fni.next()  
while tfn:

  .... some operations here ..

  tfn = assertUTR_ok(seqid, feature, tfn , haveSeenCDS)
  if (tfn.get_type() == "CDS"):
    haveSeenCDS = True

  .... more operations here ..

  tfn  = fni.next()


==== function is below ====

def assertUTR_ok(fn_seqid, fn_parent, fn , SeenCDS):
  # first let's make sure we are dealing with a UTR
  fn_type = fn.get_type()
  if not (fn_type.endswith("prime_UTR") ):
    return fn
  # Ok, now operate on this item
  fn_strand = fn.get_strand()
  fn_start,fn_end = fn.get_range()
  fn_new_type = ""

# Have SEEN CDS
  if  (SeenCDS):
    if  (fn_strand == "+"):  # we know this should be a 3'UTR
      fn_new_type = "three_prime_UTR"
    else:  # fn_strand == "-"  # should be 5'UTR
      fn_new_type = "five_prime_UTR"
      
  # Have NOT seen CDS  
  else: #  SeenCDS == False
    if (fn_strand == "+"):
      fn_new_type = "five_prime_UTR"
    else:
      fn_new_type = "three_prime_UTR"

  # Now check if labeled correctly
  if (fn_type == fn_new_type):
    return fn
  else:
    # make new copy of fn, with correct type
    new_child = FeatureNode.create_new(fn_seqid, \
		fn_new_type, fn_start, fn_end, fn_strand)
    # attach all other attributes
    new_child.set_source(fn.get_source())
    for thistag, thisval in fn.each_attribute():
      new_child.add_attribute(thistag, thisval)
    # add new_child to its parent  
    fn_parent.add_child(new_child)
    # delete offending child node
    fn.__del__()               **** <- does not seem to delete the node
    return new_child  

====


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