dirs only contains folders that has transcripts.pir files

phylosofs/phylosofs.py

@@ -446,6 +446,7 @@ def doit(
 
  # create as many directories as fasta input files
  # and inside as many fasta files as transcripts
+ dirs = []
  if not uniq and not onlyQuality:
  print("prepare intputs...")
  pathTransSeqs = os.path.abspath(pathTransSeqs)
@@ -461,6 +462,7 @@ def doit(
  exist_ok=True)
  mi.parseFromThorAxe(root, os.path.join(outputDir, root),
  onlyhuman)
+ dirs.append(root)
  # determine the number of templates that will be retained
  selTemp = ""
  for i in range(nbTemp):
@@ -472,7 +474,7 @@ def doit(
 
  # the 'if' is to not perform the modelling in __pycache__
  # might add a list of forbidden names for less errors
- dirs = [x[0] for x in os.walk('.') if not '__pycache__' in x[0]]
+ # dirs = [x[0] for x in os.walk('.') if not '__pycache__' in x[0]]
  # NOTE: dirs is at leat ['.'] and it has subfolders,
  # e.g. ['.', './folder', './folder/subfolder']
 
@@ -490,8 +492,8 @@ def doit(
  only3D, CONTEXTLIB)
  os.chdir(outputDir)
  else:
- print("Molecular modelling in: {}".format(str(dirs[1:])))
- for mydir in dirs[1:]:
+ print("Molecular modelling in: {}".format(str(dirs)))
+ for mydir in dirs:
  os.chdir(mydir)
  for trans in glob.glob('*.fasta') + glob.glob('*.faa'):
  stop = False