getIndexOfPatternInGenome.py

def indexOfPatternMatch (pattern, genome):
  indexes = []
  patternLength = len(pattern)
  for (index, _) in enumerate(genome):
    if genome[index:(patternLength+index)] == pattern:
      indexes.append(index)
  return " ".join(str(item) for item in indexes)

def loadGenome(path, pattern):
  file = open(path, 'r')
  genome = "".join(file.readlines())
  return indexOfPatternMatch(pattern ,genome)

print(loadGenome('./Downloads/Vibrio_cholerae.txt', 'CTTGATCAT'))