#!/usr/bin/env python

# Find ORFs in DNA.
# Put markup around them.

from fileinput import input
import string
import sys
import re

_orfPattern = r'ATG(...)*?(TAG|TGA|TTA)'
_orf = re.compile( _orfPattern )

def findOrfs( theSeq ):
  """Return a list of the ORFs.

  >>> findOrfs( "" )
  []

  >>> findOrfs( "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" )
  []

  >>> findOrfs( "AAATGAATAATAATGATTGAGGGG" )
  [(2, 17)]

  >>> findOrfs( "AAATGAATAATAATGATTGAGGGATGTAG" )
  [(2, 17), (23, 26)]

  """
  answer = []
  m = _orf.search( theSeq )
  while ( m ):
    answer.append( ( m.start(), m.end()-3 ) )
    m = _orf.search( theSeq, m.start()+3 )
  return answer

def markOrfs( theSeq ):
  """Mark up sequence data with ORF data.

  >>> markOrfs( "AAATGAATAATAATGATTGAGGG" )
  'AA<span class="orf"><span class="startCodon" title="Start">ATG</span>AATAATAATGAT</span><span class="stopCodon" title="Stop">TGA</span>GGG'

  """
  a = findOrfs( theSeq )
  answer = ""
  marker = 0;
  for p in a:
    if p[0] < marker: continue
    answer += theSeq[ marker: p[0] ]
    marker = p[0] + 3
    answer += '<span class="orf"><span class="startCodon" title="Start">%s</span>%s</span><span class="stopCodon" title="Stop">%s</span>' \
            % ( theSeq[ p[0]: marker ], theSeq[ marker: p[1] ], theSeq[ p[1]: p[1]+3 ] )
    marker = p[1] + 3
  answer += theSeq[ marker: ]
  return answer

#_codingRegion = re.compile( r'(?<=TATA.{1,10})ATG(...)*(TAG|TGA|TTA)' )
# sre_constants.error: look-behind requires fixed-width pattern
_codingRegion = re.compile( r'TATA.{1,30}(%s)' % _orfPattern )

def findCodingRegions( theSeq ):
  """Return a list of the ORFs that might be coding regions.

  >>> src = '''
  ... GACTATATCTTATAAACCAATGGTACCAAAACTGGAGCGTCGATGTCCGGAAATTGATAT
  ... TCTGTTCCTGACCGGGAGCTCCGCCGGAAGATTTTCACCGTATACTCGGGCACCAGGAGA
  ... TCTGCATGGAAGAGCGATGTGTCGACCGTTCCGTGGCATAACTCCGCCTAGCGGCAAAGC
  ... GAAGTTGTTTGACAGGTGATGAAAAAAACAAAAAATGTCGAACGAGTAGCGTGCATAATG
  ... AGTGCGTCAATGCTGTATTTCTGATCGTGGCGTGAATACGCGTGGTACGCCGCAAAAGCC
  ... TTATGTGCAGGAGCACTGGCGGCATCTTCTCTGTCATTTTGCCTTCAAAACG
  ... '''
  >>> src = src.replace('\\n', '')
  >>> findCodingRegions( src )
  [(19, 199), (42, 57), (125, 275)]

  """

  answer = []
  mStart = 0
  m = _codingRegion.search( theSeq, mStart )
  while ( m ):
    answer.append( m.span( 1 ) )
    mStart = m.start() + 3
    m = _codingRegion.search( theSeq, mStart )
  return answer

def markCodingRegions( theSeq ):
  """Mark up sequence data with coding region data.

       123456789 123456789 123456789 123456789 123456789 123456789
  >>> src = '''
  ... GACTATATCTTATAAACCAATGGTACCAAAACTGGAGCGTCGATGTCCGGAAATTGATAT
  ... TCTGTTCCTGACCGGGAGCTCCGCCGGAAGATTTTCACCGTATACTCGGGCACCAGGAGA
  ... TCTGCATGGAAGAGCGATGTGTCGACCGTTCCGTGGCATAACTCCGCCTAGCGGCAAAGC
  ... GAAGTTGTTTGACAGGTGATGAAAAAAACAAAAAATGTCGAACGAGTAGCGTGCATAATG
  ... AGTGCGTCAATGCTGTATTTCTGATCGTGGCGTGAATACGCGTGGTACGCCGCAAAAGCC
  ... TTATGTGCAGGAGCACTGGCGGCATCTTCTCTGTCATTTTGCCTTCAAAACG
  ... '''
  >>> src = src.replace('\\n', '')
  >>> html = markCodingRegions( src )

  >>> html[:7]
  'GACTATA'
  >>> html[-9:]
  'TTCAAAACG'
  >>> len( html )
  463

  >>> html[18:96]
  'A<span class="codingRegion"><span class="startCodon" title="Start">ATG</span>G'
  >>> html[266:313]
  'AGG</span><span class="stopCodon">TGA</span>TGA'

  >>> html[314:].index( '<' )
  Traceback (most recent call last):
  ...
  ValueError: substring not found

  """
  a = findCodingRegions( theSeq )
  answer = ""
  marker = 0;
  for p in a:
    if p[0] < marker: continue
    answer += theSeq[ marker: p[0] ]
    marker = p[0] + 3
    answer += '<span class="codingRegion"><span class="startCodon" title="Start">%s</span>%s</span><span class="stopCodon">%s</span>' \
          % ( theSeq[ p[0]: marker ], theSeq[ marker: p[1]-3 ], theSeq[ p[1]-3: p[1] ] )
    marker = p[1]
  answer += theSeq[ marker: ]
  return answer

def _markEm( theInput ):
  for line in theInput:
    print markCodingRegions( line )

def _testdoc():
  import doctest
  doctest.testmod()

if __name__ == '__main__':
  if 1 < len( sys.argv ):
    if "doctest" == sys.argv[1]:
      _testdoc()
    else:
      try:
        f = open( sys.argv[1] )
      except IOError, e:
        print e
      else:
        _markEm( f )
        f.close()
        
  else:
    _markEm( input() )