new_contents: #for a directory of FASTA gene family files, compute a gene presence-absence (or Count-type) table
  from __future__ import print_function
  import os, re
  
  to_check = [file for file in os.listdir("fasta/") if file.endswith(".fa")]
  #first obtain a complete list of the species. This is an appalling inefficient "algorithm"
  species = {}
  for file in to_check:
      inh = open("fasta/" + file)
      for line in inh:
          if line.startswith(">"):
              fields = re.split("_", line[1:])
              sp = fields[0]
              species[sp] = 1
  
  #...and now, read the sequence files one at a time and print out a line corresponding to the count profile
  
  splist = species.keys()
  print("Family\t", end = '')
  for element in splist:
      print(element + "\t", end='')
  print("\n", end = '')
  
  for file in to_check:
      file_count = {}
      inh = open("fasta/" + file)
      for line in inh:
          fields = re.split("_", line[1:])
          if fields[0] in file_count:
              file_count[fields[0]] += 1
          else:
              file_count[fields[0]] = 1
      print(file + "\t", end = '')
      for sp in splist:
          if sp in file_count:
              print(str(file_count[sp]) + "\t", end = '')
          else:
              print("0\t", end = '')
      print("\n", end = '') 
  
subject: Print a presence/absence table from a directory of FASTA-formatted sequence files