old_contents: #!/usr/bin/env python3
  """Test initializing Yang's Random Walk Contribution initialization"""
  
  __copyright__ = "Copyright (C) 2019-2020, DV Klopfenstein, H Tang. All rights reserved."
  __author__ = "DV Klopfenstein"
  
  import os
  import sys
  import timeit
  from datetime import timedelta
  from goatools.base import get_godag as base_get_godag
  from goatools.associations import dnld_annotation
  from goatools.anno.factory import get_objanno as get_objanno_factory
  # from goatools.gosubdag.gosubdag import GoSubDag
  from goatools.semantic import TermCounts
  
  # from goatools_alpha.geneprodsim.semanticcalcs import SemanticCalcs
  
  REPO = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
  
  def prt_hms(tic, msg, prt=sys.stdout):
      """Print elapsed time and return current time"""
      toc = timeit.default_timer()
      prt.write('{HMS} {MSG}\n'.format(HMS=str(timedelta(seconds=toc-tic)), MSG=msg))
      return toc
  
  def get_godag(fin_godag, **kws):
      """Get GODAG containing only primary GO IDs (no alternate GO IDs)"""
      godag = base_get_godag(os.path.join(REPO, fin_godag), loading_bar=False, **kws)
      return {o.item_id:o for o in godag.values()}
  
  def get_anno_fullname(fin_anno):
      """Get annotation filename"""
      fin_full = os.path.join(REPO, fin_anno)
      dnld_annotation(fin_full)
      return fin_full
  
  def get_objanno(fin_anno, godag, namespace='all'):
      """Get annotation object"""
      fin_full = get_anno_fullname(fin_anno)
      return get_objanno_factory(fin_full, godag=godag, namespace=namespace)
  
  def get_termcounts(fin_anno, godag, namespace='all', **kws):
      """Get termcounts object"""
      objanno = get_objanno(fin_anno, godag, namespace)
      id2gos = objanno.get_id2gos(namespace=namespace, **kws)
      return TermCounts(godag, id2gos)
  
  
  # Copyright (C) 2019-2020, DV Klopfenstein, et al. All rights reserved.
  
new_contents: #!/usr/bin/env python3
  """Test initializing Yang's Random Walk Contribution initialization"""
  
  __copyright__ = "Copyright (C) 2019-2020, DV Klopfenstein, H Tang. All rights reserved."
  __author__ = "DV Klopfenstein"
  
  import os
  import sys
  import timeit
  from datetime import timedelta
  from goatools.base import get_godag as base_get_godag
  from goatools.associations import dnld_annotation
  from goatools.anno.factory import get_objanno as get_objanno_factory
  # from goatools.gosubdag.gosubdag import GoSubDag
  from goatools.semantic import TermCounts
  
  # from goatools_alpha.geneprodsim.semanticcalcs import SemanticCalcs
  
  REPO = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")
  
  def prt_hms(tic, msg, prt=sys.stdout):
      """Print elapsed time and return current time"""
      toc = timeit.default_timer()
      prt.write('{HMS} {MSG}\n'.format(HMS=str(timedelta(seconds=toc-tic)), MSG=msg))
      return toc
  
  def repofn(fin):
      """Get a full filename, given a local file name from repo dir root"""
      return os.path.join(REPO, fin)
  
  def get_godag(fin_godag, **kws):
      """Get GODAG containing only primary GO IDs (no alternate GO IDs)"""
      godag = base_get_godag(os.path.join(REPO, fin_godag), loading_bar=False, **kws)
      return {o.item_id:o for o in godag.values()}
  
  def get_anno_fullname(fin_anno):
      """Get annotation filename"""
      fin_full = os.path.join(REPO, fin_anno)
      dnld_annotation(fin_full)
      return fin_full
  
  def get_objanno(fin_anno, godag, namespace='all'):
      """Get annotation object"""
      fin_full = get_anno_fullname(fin_anno)
      return get_objanno_factory(fin_full, godag=godag, namespace=namespace)
  
  def get_termcounts(fin_anno, godag, namespace='all', **kws):
      """Get termcounts object"""
      objanno = get_objanno(fin_anno, godag, namespace)
      id2gos = objanno.get_id2gos(namespace=namespace, **kws)
      return TermCounts(godag, id2gos)
  
  
  # Copyright (C) 2019-2020, DV Klopfenstein, et al. All rights reserved.
  
subject: Add function to get full filename