# -*- coding: utf-8 -*-

__abstract__  = 'Genotype representation parsers for text file input/output'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__   = 'See GLU license for terms by running: glu license'
__revision__  = '$Id$'

from   operator                   import getitem
from   itertools                  import imap, repeat


class Nothing(object): pass

# Glossary of terms:
#   genotype tuple  = tuple of two alleles or None if missing.
#   internal rep    = opaque object representing a genotype,
#                     evaluates to False iff missing
#   genotype string = string representation
#   packed          = random access sequence of internal genotype reps


class UnphasedMarkerRepresentation(object):
  '''
  Generic unphased marker representation where the genotype representation
  and internal representation are the same.
  '''

  def __init__(self, missing_geno_str=Nothing, missing_geno_strs=(),
                     missing_allele_str='',    missing_allele_strs=(),
                     delimiter='/'):
    '''
    Construct a new UnphasedMarkerRepresentation

    This class represents bidirectional mappings of genotypes between
    strings and Python objects.  The object representation of a genotype is
    a tuple of two alleles, with the missing genotype being None or any
    other object that evaluates to False.  Given this representation,
    alleles need not be known in advance.  The "internal representation" is
    the same as the Python object representation (for an example of a non-
    trivial internal representation see UnphasedMarkerRepresentation
    below).

    @param    missing_geno_str: canonical missing genotype output string representation, optional
                                and defaults to Nothing
    @type     missing_geno_str: str
    @param   missing_geno_strs: missing genotype input strings
    @type    missing_geno_strs: sequence
    @param  missing_allele_str: canonical missing allele output string representation, default is ''
                                and defaults to an empty string
    @type   missing_allele_str: str
    @param missing_allele_strs: missing allele input strings
    @type  missing_allele_strs: sequence
    @param           delimiter: allele delimiter for genotypes, defaults is '/'
    @type            delimiter: str
    '''
    self.missing_geno_str    = missing_geno_str
    self.missing_geno_strs   = missing_geno_strs
    self.missing_allele_str  = missing_allele_str
    self.missing_allele_strs = missing_allele_strs
    self.delimiter           = delimiter

    self.allelerep  = {None:self.missing_allele_str}
    self.allelestr  = dict( (m,None) for m in missing_allele_strs )
    self.missing    = None
    self.strcache   = {}

  def to_string(self, rep):
    '''
    Transform a genotype in internal format to a genotype string

    @param rep: genotype in internal format
    @type  rep: object
    @return   : genotype in string format
    @rtype    : str

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> snp.to_string( model['A','A'] )
    'AA'
    >>> snp.to_string( model[None, 'A'] )
    ' A'
    >>> snp.to_string( model['A', None] )
    ' A'
    >>> snp.to_string( model[None,None])
    '  '
    >>> hapmap.to_string( model['A','A'] )
    'AA'
    >>> hapmap.to_string( model[None, 'A'] )
    'NA'
    >>> hapmap.to_string( model['A', None] )
    'NA'
    >>> hapmap.to_string( model[None,None])
    'NN'
    >>> marker.to_string( model['A','A'] )
    'A/A'
    >>> marker.to_string( model[None, 'A'] )
    '/A'
    >>> marker.to_string( model['A', None] )
    '/A'
    >>> marker.to_string( model[None,None])
    ''
    '''
    # Macro-optimized
    #return self.to_string_from_alleles(rep.alleles())
    rep = rep.alleles()
    strcache = self.strcache
    if rep in strcache:
      return strcache[rep]

    if rep == (None,None):
      if self.missing_geno_str is not Nothing:
        return self.missing_geno_str

    alleles = [ self.allelerep.setdefault(a,a) for a in rep ]

    if not self.delimiter:
      for a in alleles:
        if len(a) > 1:
         raise ValueError('Invalid genotype representation')

    gstr = strcache[rep] = self.delimiter.join(alleles)
    return gstr

  def to_string_from_alleles(self,rep):
    '''
    Transform a genotype tuple to a genotype string

    @param rep: genotype in tuple format
    @type  rep: object
    @return   : genotype in string format
    @rtype    : str

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> snp.to_string_from_alleles( ('A','A') )
    'AA'
    >>> snp.to_string_from_alleles( (None, 'A') )
    ' A'
    >>> snp.to_string_from_alleles( ('A', None) )
    'A '
    >>> snp.to_string_from_alleles( (None,None))
    '  '
    >>> hapmap.to_string_from_alleles( ('A','A') )
    'AA'
    >>> hapmap.to_string_from_alleles( (None, 'A') )
    'NA'
    >>> hapmap.to_string_from_alleles( ('A', None) )
    'AN'
    >>> hapmap.to_string_from_alleles( (None,None))
    'NN'
    >>> marker.to_string_from_alleles( ('A','A') )
    'A/A'
    >>> marker.to_string_from_alleles( (None, 'A') )
    '/A'
    >>> marker.to_string_from_alleles( ('A', None) )
    'A/'
    >>> marker.to_string_from_alleles( (None,None))
    ''
    '''
    strcache = self.strcache
    if rep in strcache:
      return strcache[rep]

    if rep == (None,None):
      if self.missing_geno_str is not Nothing:
        return self.missing_geno_str

    alleles = [ self.allelerep.setdefault(a,a) for a in rep ]

    if not self.delimiter:
      for a in alleles:
        if len(a) > 1:
         raise ValueError('Invalid genotype representation')

    gstr = strcache[rep] = self.delimiter.join(alleles)
    return gstr

  def to_strings(self,reps):
    '''
    Transform a sequence of genotypes in internal format to a genotype strings

    @param reps: genotypes in internal format
    @type  reps: sequence
    @return    : genotypes in string format
    @rtype     : sequence

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> genos = [ model[g] for g in [('A','A'),(None,'A'),(None,None)] ]
    >>> snp.to_strings(genos)
    ['AA', ' A', '  ']
    >>> hapmap.to_strings(genos)
    ['AA', 'NA', 'NN']
    >>> marker.to_strings(genos)
    ['A/A', '/A', '']
    '''
    try:
      strcache = self.strcache
      return [ strcache[r.alleles()] for r in reps ]
    except KeyError:
      return map(self.to_string, reps)

  def from_string(self, geno):
    '''
    Transform a genotype string to internal format

    @param geno: genotype string
    @type  geno: str
    @return    : genotype in internal format
    @rtype     : object

    >>> snp.from_string('AA')
    ('A', 'A')
    >>> snp.from_string('AB')
    ('A', 'B')
    >>> snp.from_string('BA')
    ('A', 'B')
    >>> snp.from_string(' A')
    (None, 'A')
    >>> snp.from_string('A ')
    (None, 'A')
    >>> snp.from_string('  ')
    (None, None)
    >>> snp.from_string('')
    (None, None)

    >>> hapmap.from_string('AA')
    ('A', 'A')
    >>> hapmap.from_string('AB')
    ('A', 'B')
    >>> hapmap.from_string('BA')
    ('A', 'B')
    >>> hapmap.from_string('NA')
    (None, 'A')
    >>> hapmap.from_string('AN')
    (None, 'A')
    >>> hapmap.from_string('NN')
    (None, None)

    >>> marker.from_string('A/A')
    ('A', 'A')
    >>> marker.from_string('A/B')
    ('A', 'B')
    >>> marker.from_string('B/A')
    ('A', 'B')
    >>> marker.from_string(' /A')
    (None, 'A')
    >>> marker.from_string('/A')
    (None, 'A')
    >>> marker.from_string('A/ ')
    (None, 'A')
    >>> marker.from_string('A/')
    (None, 'A')
    >>> marker.from_string(' / ')
    (None, None)
    >>> marker.from_string('/')
    (None, None)
    >>> marker.from_string('/ ')
    (None, None)
    >>> marker.from_string(' /')
    (None, None)
    >>> marker.from_string('')
    (None, None)
    '''
    strcache = self.strcache
    if geno in strcache:
      return strcache[geno]

    if geno in self.missing_geno_strs:
      rep = self.strcache[geno] = (None,None)
      return rep

    if self.delimiter:
      alleles = geno.split(self.delimiter)
    else:
      alleles = geno

    if len(alleles) != 2:
      raise ValueError('Invalid genotype: %s' % geno)

    rep = self.strcache[intern(geno)] = \
          tuple(sorted(self.allelestr.setdefault(a,a) for a in alleles))

    return rep

  def from_strings(self,genos):
    '''
    Transform a sequence of genotype strings to internal format

    @param genos: sequence of genotype strings
    @type  genos: sequence of str
    @return     : sequence of genotype in internal format
    @rtype      : sequence of objects

    >>> snp.from_strings(['AA','AB','BA',' A','A ','  ',''])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None), (None, None)]
    >>> hapmap.from_strings(['AA','AB','BA','NA','AN','NN'])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None)]
    >>> marker.from_strings(['A/A','A/B','B/A',' /A','A/ ',' / ',''])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None), (None, None)]
    '''
    try:
      return list(imap(getitem, repeat(self.strcache), genos))
    except KeyError:
      return map(self.from_string, genos)


# GLU native SNP format
snp    = UnphasedMarkerRepresentation(delimiter='', missing_geno_str='  ',missing_geno_strs=['','  '],
                                      missing_allele_str=' ',missing_allele_strs=['',' '])
# Illumina SNP data from BeadStudio
isnp   = UnphasedMarkerRepresentation(delimiter='', missing_geno_str='--',missing_geno_strs=['','--'],
                                      missing_allele_str='-',missing_allele_strs=['-'])

# HapMap SNP format
hapmap = UnphasedMarkerRepresentation(delimiter='',missing_geno_str='NN',missing_geno_strs=['','NN'],
                                      missing_allele_str='N',missing_allele_strs=['N'],)

# Delimited marker format using a slash
marker = UnphasedMarkerRepresentation(delimiter='/',missing_geno_str='',missing_geno_strs=['','/'],
                                      missing_allele_str='',missing_allele_strs=['',' '])


def get_genorepr(reprname):
  '''
  Retrieve the supported genotype representation. Otherwise raises an ValueError exception

  @param reprname: internal genotype representation
  @type  reprname: str
  @return        : supported genotype representation
  @rtype         : genotype representation object
  '''

  reprs = { 'snp'    : snp,
            'isnp'   : isnp,
            'hapmap' : hapmap,
            'marker' : marker }

  if not reprname:
    reprname = 'snp'

  try:
    return reprs[reprname]
  except KeyError:
    raise ValueError('Unknown genotype representation: %s' % reprname)


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


if __name__ == '__main__':
  main()

24f6dc3ef82370b288673dd5822791c93c6cb811
<mask token>


class Nothing(object):
    pass


class UnphasedMarkerRepresentation(object):
    """
  Generic unphased marker representation where the genotype representation
  and internal representation are the same.
  """

    def __init__(self, missing_geno_str=Nothing, missing_geno_strs=(),
        missing_allele_str='', missing_allele_strs=(), delimiter='/'):
        """
    Construct a new UnphasedMarkerRepresentation

    This class represents bidirectional mappings of genotypes between
    strings and Python objects.  The object representation of a genotype is
    a tuple of two alleles, with the missing genotype being None or any
    other object that evaluates to False.  Given this representation,
    alleles need not be known in advance.  The "internal representation" is
    the same as the Python object representation (for an example of a non-
    trivial internal representation see UnphasedMarkerRepresentation
    below).

    @param    missing_geno_str: canonical missing genotype output string representation, optional
                                and defaults to Nothing
    @type     missing_geno_str: str
    @param   missing_geno_strs: missing genotype input strings
    @type    missing_geno_strs: sequence
    @param  missing_allele_str: canonical missing allele output string representation, default is ''
                                and defaults to an empty string
    @type   missing_allele_str: str
    @param missing_allele_strs: missing allele input strings
    @type  missing_allele_strs: sequence
    @param           delimiter: allele delimiter for genotypes, defaults is '/'
    @type            delimiter: str
    """
        self.missing_geno_str = missing_geno_str
        self.missing_geno_strs = missing_geno_strs
        self.missing_allele_str = missing_allele_str
        self.missing_allele_strs = missing_allele_strs
        self.delimiter = delimiter
        self.allelerep = {None: self.missing_allele_str}
        self.allelestr = dict((m, None) for m in missing_allele_strs)
        self.missing = None
        self.strcache = {}

    def to_string(self, rep):
        """
    Transform a genotype in internal format to a genotype string

    @param rep: genotype in internal format
    @type  rep: object
    @return   : genotype in string format
    @rtype    : str

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> snp.to_string( model['A','A'] )
    'AA'
    >>> snp.to_string( model[None, 'A'] )
    ' A'
    >>> snp.to_string( model['A', None] )
    ' A'
    >>> snp.to_string( model[None,None])
    '  '
    >>> hapmap.to_string( model['A','A'] )
    'AA'
    >>> hapmap.to_string( model[None, 'A'] )
    'NA'
    >>> hapmap.to_string( model['A', None] )
    'NA'
    >>> hapmap.to_string( model[None,None])
    'NN'
    >>> marker.to_string( model['A','A'] )
    'A/A'
    >>> marker.to_string( model[None, 'A'] )
    '/A'
    >>> marker.to_string( model['A', None] )
    '/A'
    >>> marker.to_string( model[None,None])
    ''
    """
        rep = rep.alleles()
        strcache = self.strcache
        if rep in strcache:
            return strcache[rep]
        if rep == (None, None):
            if self.missing_geno_str is not Nothing:
                return self.missing_geno_str
        alleles = [self.allelerep.setdefault(a, a) for a in rep]
        if not self.delimiter:
            for a in alleles:
                if len(a) > 1:
                    raise ValueError('Invalid genotype representation')
        gstr = strcache[rep] = self.delimiter.join(alleles)
        return gstr

    def to_string_from_alleles(self, rep):
        """
    Transform a genotype tuple to a genotype string

    @param rep: genotype in tuple format
    @type  rep: object
    @return   : genotype in string format
    @rtype    : str

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> snp.to_string_from_alleles( ('A','A') )
    'AA'
    >>> snp.to_string_from_alleles( (None, 'A') )
    ' A'
    >>> snp.to_string_from_alleles( ('A', None) )
    'A '
    >>> snp.to_string_from_alleles( (None,None))
    '  '
    >>> hapmap.to_string_from_alleles( ('A','A') )
    'AA'
    >>> hapmap.to_string_from_alleles( (None, 'A') )
    'NA'
    >>> hapmap.to_string_from_alleles( ('A', None) )
    'AN'
    >>> hapmap.to_string_from_alleles( (None,None))
    'NN'
    >>> marker.to_string_from_alleles( ('A','A') )
    'A/A'
    >>> marker.to_string_from_alleles( (None, 'A') )
    '/A'
    >>> marker.to_string_from_alleles( ('A', None) )
    'A/'
    >>> marker.to_string_from_alleles( (None,None))
    ''
    """
        strcache = self.strcache
        if rep in strcache:
            return strcache[rep]
        if rep == (None, None):
            if self.missing_geno_str is not Nothing:
                return self.missing_geno_str
        alleles = [self.allelerep.setdefault(a, a) for a in rep]
        if not self.delimiter:
            for a in alleles:
                if len(a) > 1:
                    raise ValueError('Invalid genotype representation')
        gstr = strcache[rep] = self.delimiter.join(alleles)
        return gstr

    def to_strings(self, reps):
        """
    Transform a sequence of genotypes in internal format to a genotype strings

    @param reps: genotypes in internal format
    @type  reps: sequence
    @return    : genotypes in string format
    @rtype     : sequence

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> genos = [ model[g] for g in [('A','A'),(None,'A'),(None,None)] ]
    >>> snp.to_strings(genos)
    ['AA', ' A', '  ']
    >>> hapmap.to_strings(genos)
    ['AA', 'NA', 'NN']
    >>> marker.to_strings(genos)
    ['A/A', '/A', '']
    """
        try:
            strcache = self.strcache
            return [strcache[r.alleles()] for r in reps]
        except KeyError:
            return map(self.to_string, reps)

    def from_string(self, geno):
        """
    Transform a genotype string to internal format

    @param geno: genotype string
    @type  geno: str
    @return    : genotype in internal format
    @rtype     : object

    >>> snp.from_string('AA')
    ('A', 'A')
    >>> snp.from_string('AB')
    ('A', 'B')
    >>> snp.from_string('BA')
    ('A', 'B')
    >>> snp.from_string(' A')
    (None, 'A')
    >>> snp.from_string('A ')
    (None, 'A')
    >>> snp.from_string('  ')
    (None, None)
    >>> snp.from_string('')
    (None, None)

    >>> hapmap.from_string('AA')
    ('A', 'A')
    >>> hapmap.from_string('AB')
    ('A', 'B')
    >>> hapmap.from_string('BA')
    ('A', 'B')
    >>> hapmap.from_string('NA')
    (None, 'A')
    >>> hapmap.from_string('AN')
    (None, 'A')
    >>> hapmap.from_string('NN')
    (None, None)

    >>> marker.from_string('A/A')
    ('A', 'A')
    >>> marker.from_string('A/B')
    ('A', 'B')
    >>> marker.from_string('B/A')
    ('A', 'B')
    >>> marker.from_string(' /A')
    (None, 'A')
    >>> marker.from_string('/A')
    (None, 'A')
    >>> marker.from_string('A/ ')
    (None, 'A')
    >>> marker.from_string('A/')
    (None, 'A')
    >>> marker.from_string(' / ')
    (None, None)
    >>> marker.from_string('/')
    (None, None)
    >>> marker.from_string('/ ')
    (None, None)
    >>> marker.from_string(' /')
    (None, None)
    >>> marker.from_string('')
    (None, None)
    """
        strcache = self.strcache
        if geno in strcache:
            return strcache[geno]
        if geno in self.missing_geno_strs:
            rep = self.strcache[geno] = None, None
            return rep
        if self.delimiter:
            alleles = geno.split(self.delimiter)
        else:
            alleles = geno
        if len(alleles) != 2:
            raise ValueError('Invalid genotype: %s' % geno)
        rep = self.strcache[intern(geno)] = tuple(sorted(self.allelestr.
            setdefault(a, a) for a in alleles))
        return rep

    def from_strings(self, genos):
        """
    Transform a sequence of genotype strings to internal format

    @param genos: sequence of genotype strings
    @type  genos: sequence of str
    @return     : sequence of genotype in internal format
    @rtype      : sequence of objects

    >>> snp.from_strings(['AA','AB','BA',' A','A ','  ',''])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None), (None, None)]
    >>> hapmap.from_strings(['AA','AB','BA','NA','AN','NN'])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None)]
    >>> marker.from_strings(['A/A','A/B','B/A',' /A','A/ ',' / ',''])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None), (None, None)]
    """
        try:
            return list(imap(getitem, repeat(self.strcache), genos))
        except KeyError:
            return map(self.from_string, genos)


<mask token>

<mask token>


class Nothing(object):
    pass


class UnphasedMarkerRepresentation(object):
    """
  Generic unphased marker representation where the genotype representation
  and internal representation are the same.
  """

    def __init__(self, missing_geno_str=Nothing, missing_geno_strs=(),
        missing_allele_str='', missing_allele_strs=(), delimiter='/'):
        """
    Construct a new UnphasedMarkerRepresentation

    This class represents bidirectional mappings of genotypes between
    strings and Python objects.  The object representation of a genotype is
    a tuple of two alleles, with the missing genotype being None or any
    other object that evaluates to False.  Given this representation,
    alleles need not be known in advance.  The "internal representation" is
    the same as the Python object representation (for an example of a non-
    trivial internal representation see UnphasedMarkerRepresentation
    below).

    @param    missing_geno_str: canonical missing genotype output string representation, optional
                                and defaults to Nothing
    @type     missing_geno_str: str
    @param   missing_geno_strs: missing genotype input strings
    @type    missing_geno_strs: sequence
    @param  missing_allele_str: canonical missing allele output string representation, default is ''
                                and defaults to an empty string
    @type   missing_allele_str: str
    @param missing_allele_strs: missing allele input strings
    @type  missing_allele_strs: sequence
    @param           delimiter: allele delimiter for genotypes, defaults is '/'
    @type            delimiter: str
    """
        self.missing_geno_str = missing_geno_str
        self.missing_geno_strs = missing_geno_strs
        self.missing_allele_str = missing_allele_str
        self.missing_allele_strs = missing_allele_strs
        self.delimiter = delimiter
        self.allelerep = {None: self.missing_allele_str}
        self.allelestr = dict((m, None) for m in missing_allele_strs)
        self.missing = None
        self.strcache = {}

    def to_string(self, rep):
        """
    Transform a genotype in internal format to a genotype string

    @param rep: genotype in internal format
    @type  rep: object
    @return   : genotype in string format
    @rtype    : str

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> snp.to_string( model['A','A'] )
    'AA'
    >>> snp.to_string( model[None, 'A'] )
    ' A'
    >>> snp.to_string( model['A', None] )
    ' A'
    >>> snp.to_string( model[None,None])
    '  '
    >>> hapmap.to_string( model['A','A'] )
    'AA'
    >>> hapmap.to_string( model[None, 'A'] )
    'NA'
    >>> hapmap.to_string( model['A', None] )
    'NA'
    >>> hapmap.to_string( model[None,None])
    'NN'
    >>> marker.to_string( model['A','A'] )
    'A/A'
    >>> marker.to_string( model[None, 'A'] )
    '/A'
    >>> marker.to_string( model['A', None] )
    '/A'
    >>> marker.to_string( model[None,None])
    ''
    """
        rep = rep.alleles()
        strcache = self.strcache
        if rep in strcache:
            return strcache[rep]
        if rep == (None, None):
            if self.missing_geno_str is not Nothing:
                return self.missing_geno_str
        alleles = [self.allelerep.setdefault(a, a) for a in rep]
        if not self.delimiter:
            for a in alleles:
                if len(a) > 1:
                    raise ValueError('Invalid genotype representation')
        gstr = strcache[rep] = self.delimiter.join(alleles)
        return gstr

    def to_string_from_alleles(self, rep):
        """
    Transform a genotype tuple to a genotype string

    @param rep: genotype in tuple format
    @type  rep: object
    @return   : genotype in string format
    @rtype    : str

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> snp.to_string_from_alleles( ('A','A') )
    'AA'
    >>> snp.to_string_from_alleles( (None, 'A') )
    ' A'
    >>> snp.to_string_from_alleles( ('A', None) )
    'A '
    >>> snp.to_string_from_alleles( (None,None))
    '  '
    >>> hapmap.to_string_from_alleles( ('A','A') )
    'AA'
    >>> hapmap.to_string_from_alleles( (None, 'A') )
    'NA'
    >>> hapmap.to_string_from_alleles( ('A', None) )
    'AN'
    >>> hapmap.to_string_from_alleles( (None,None))
    'NN'
    >>> marker.to_string_from_alleles( ('A','A') )
    'A/A'
    >>> marker.to_string_from_alleles( (None, 'A') )
    '/A'
    >>> marker.to_string_from_alleles( ('A', None) )
    'A/'
    >>> marker.to_string_from_alleles( (None,None))
    ''
    """
        strcache = self.strcache
        if rep in strcache:
            return strcache[rep]
        if rep == (None, None):
            if self.missing_geno_str is not Nothing:
                return self.missing_geno_str
        alleles = [self.allelerep.setdefault(a, a) for a in rep]
        if not self.delimiter:
            for a in alleles:
                if len(a) > 1:
                    raise ValueError('Invalid genotype representation')
        gstr = strcache[rep] = self.delimiter.join(alleles)
        return gstr

    def to_strings(self, reps):
        """
    Transform a sequence of genotypes in internal format to a genotype strings

    @param reps: genotypes in internal format
    @type  reps: sequence
    @return    : genotypes in string format
    @rtype     : sequence

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> genos = [ model[g] for g in [('A','A'),(None,'A'),(None,None)] ]
    >>> snp.to_strings(genos)
    ['AA', ' A', '  ']
    >>> hapmap.to_strings(genos)
    ['AA', 'NA', 'NN']
    >>> marker.to_strings(genos)
    ['A/A', '/A', '']
    """
        try:
            strcache = self.strcache
            return [strcache[r.alleles()] for r in reps]
        except KeyError:
            return map(self.to_string, reps)

    def from_string(self, geno):
        """
    Transform a genotype string to internal format

    @param geno: genotype string
    @type  geno: str
    @return    : genotype in internal format
    @rtype     : object

    >>> snp.from_string('AA')
    ('A', 'A')
    >>> snp.from_string('AB')
    ('A', 'B')
    >>> snp.from_string('BA')
    ('A', 'B')
    >>> snp.from_string(' A')
    (None, 'A')
    >>> snp.from_string('A ')
    (None, 'A')
    >>> snp.from_string('  ')
    (None, None)
    >>> snp.from_string('')
    (None, None)

    >>> hapmap.from_string('AA')
    ('A', 'A')
    >>> hapmap.from_string('AB')
    ('A', 'B')
    >>> hapmap.from_string('BA')
    ('A', 'B')
    >>> hapmap.from_string('NA')
    (None, 'A')
    >>> hapmap.from_string('AN')
    (None, 'A')
    >>> hapmap.from_string('NN')
    (None, None)

    >>> marker.from_string('A/A')
    ('A', 'A')
    >>> marker.from_string('A/B')
    ('A', 'B')
    >>> marker.from_string('B/A')
    ('A', 'B')
    >>> marker.from_string(' /A')
    (None, 'A')
    >>> marker.from_string('/A')
    (None, 'A')
    >>> marker.from_string('A/ ')
    (None, 'A')
    >>> marker.from_string('A/')
    (None, 'A')
    >>> marker.from_string(' / ')
    (None, None)
    >>> marker.from_string('/')
    (None, None)
    >>> marker.from_string('/ ')
    (None, None)
    >>> marker.from_string(' /')
    (None, None)
    >>> marker.from_string('')
    (None, None)
    """
        strcache = self.strcache
        if geno in strcache:
            return strcache[geno]
        if geno in self.missing_geno_strs:
            rep = self.strcache[geno] = None, None
            return rep
        if self.delimiter:
            alleles = geno.split(self.delimiter)
        else:
            alleles = geno
        if len(alleles) != 2:
            raise ValueError('Invalid genotype: %s' % geno)
        rep = self.strcache[intern(geno)] = tuple(sorted(self.allelestr.
            setdefault(a, a) for a in alleles))
        return rep

    def from_strings(self, genos):
        """
    Transform a sequence of genotype strings to internal format

    @param genos: sequence of genotype strings
    @type  genos: sequence of str
    @return     : sequence of genotype in internal format
    @rtype      : sequence of objects

    >>> snp.from_strings(['AA','AB','BA',' A','A ','  ',''])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None), (None, None)]
    >>> hapmap.from_strings(['AA','AB','BA','NA','AN','NN'])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None)]
    >>> marker.from_strings(['A/A','A/B','B/A',' /A','A/ ',' / ',''])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None), (None, None)]
    """
        try:
            return list(imap(getitem, repeat(self.strcache), genos))
        except KeyError:
            return map(self.from_string, genos)


<mask token>


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


<mask token>

<mask token>


class Nothing(object):
    pass


class UnphasedMarkerRepresentation(object):
    """
  Generic unphased marker representation where the genotype representation
  and internal representation are the same.
  """

    def __init__(self, missing_geno_str=Nothing, missing_geno_strs=(),
        missing_allele_str='', missing_allele_strs=(), delimiter='/'):
        """
    Construct a new UnphasedMarkerRepresentation

    This class represents bidirectional mappings of genotypes between
    strings and Python objects.  The object representation of a genotype is
    a tuple of two alleles, with the missing genotype being None or any
    other object that evaluates to False.  Given this representation,
    alleles need not be known in advance.  The "internal representation" is
    the same as the Python object representation (for an example of a non-
    trivial internal representation see UnphasedMarkerRepresentation
    below).

    @param    missing_geno_str: canonical missing genotype output string representation, optional
                                and defaults to Nothing
    @type     missing_geno_str: str
    @param   missing_geno_strs: missing genotype input strings
    @type    missing_geno_strs: sequence
    @param  missing_allele_str: canonical missing allele output string representation, default is ''
                                and defaults to an empty string
    @type   missing_allele_str: str
    @param missing_allele_strs: missing allele input strings
    @type  missing_allele_strs: sequence
    @param           delimiter: allele delimiter for genotypes, defaults is '/'
    @type            delimiter: str
    """
        self.missing_geno_str = missing_geno_str
        self.missing_geno_strs = missing_geno_strs
        self.missing_allele_str = missing_allele_str
        self.missing_allele_strs = missing_allele_strs
        self.delimiter = delimiter
        self.allelerep = {None: self.missing_allele_str}
        self.allelestr = dict((m, None) for m in missing_allele_strs)
        self.missing = None
        self.strcache = {}

    def to_string(self, rep):
        """
    Transform a genotype in internal format to a genotype string

    @param rep: genotype in internal format
    @type  rep: object
    @return   : genotype in string format
    @rtype    : str

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> snp.to_string( model['A','A'] )
    'AA'
    >>> snp.to_string( model[None, 'A'] )
    ' A'
    >>> snp.to_string( model['A', None] )
    ' A'
    >>> snp.to_string( model[None,None])
    '  '
    >>> hapmap.to_string( model['A','A'] )
    'AA'
    >>> hapmap.to_string( model[None, 'A'] )
    'NA'
    >>> hapmap.to_string( model['A', None] )
    'NA'
    >>> hapmap.to_string( model[None,None])
    'NN'
    >>> marker.to_string( model['A','A'] )
    'A/A'
    >>> marker.to_string( model[None, 'A'] )
    '/A'
    >>> marker.to_string( model['A', None] )
    '/A'
    >>> marker.to_string( model[None,None])
    ''
    """
        rep = rep.alleles()
        strcache = self.strcache
        if rep in strcache:
            return strcache[rep]
        if rep == (None, None):
            if self.missing_geno_str is not Nothing:
                return self.missing_geno_str
        alleles = [self.allelerep.setdefault(a, a) for a in rep]
        if not self.delimiter:
            for a in alleles:
                if len(a) > 1:
                    raise ValueError('Invalid genotype representation')
        gstr = strcache[rep] = self.delimiter.join(alleles)
        return gstr

    def to_string_from_alleles(self, rep):
        """
    Transform a genotype tuple to a genotype string

    @param rep: genotype in tuple format
    @type  rep: object
    @return   : genotype in string format
    @rtype    : str

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> snp.to_string_from_alleles( ('A','A') )
    'AA'
    >>> snp.to_string_from_alleles( (None, 'A') )
    ' A'
    >>> snp.to_string_from_alleles( ('A', None) )
    'A '
    >>> snp.to_string_from_alleles( (None,None))
    '  '
    >>> hapmap.to_string_from_alleles( ('A','A') )
    'AA'
    >>> hapmap.to_string_from_alleles( (None, 'A') )
    'NA'
    >>> hapmap.to_string_from_alleles( ('A', None) )
    'AN'
    >>> hapmap.to_string_from_alleles( (None,None))
    'NN'
    >>> marker.to_string_from_alleles( ('A','A') )
    'A/A'
    >>> marker.to_string_from_alleles( (None, 'A') )
    '/A'
    >>> marker.to_string_from_alleles( ('A', None) )
    'A/'
    >>> marker.to_string_from_alleles( (None,None))
    ''
    """
        strcache = self.strcache
        if rep in strcache:
            return strcache[rep]
        if rep == (None, None):
            if self.missing_geno_str is not Nothing:
                return self.missing_geno_str
        alleles = [self.allelerep.setdefault(a, a) for a in rep]
        if not self.delimiter:
            for a in alleles:
                if len(a) > 1:
                    raise ValueError('Invalid genotype representation')
        gstr = strcache[rep] = self.delimiter.join(alleles)
        return gstr

    def to_strings(self, reps):
        """
    Transform a sequence of genotypes in internal format to a genotype strings

    @param reps: genotypes in internal format
    @type  reps: sequence
    @return    : genotypes in string format
    @rtype     : sequence

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> genos = [ model[g] for g in [('A','A'),(None,'A'),(None,None)] ]
    >>> snp.to_strings(genos)
    ['AA', ' A', '  ']
    >>> hapmap.to_strings(genos)
    ['AA', 'NA', 'NN']
    >>> marker.to_strings(genos)
    ['A/A', '/A', '']
    """
        try:
            strcache = self.strcache
            return [strcache[r.alleles()] for r in reps]
        except KeyError:
            return map(self.to_string, reps)

    def from_string(self, geno):
        """
    Transform a genotype string to internal format

    @param geno: genotype string
    @type  geno: str
    @return    : genotype in internal format
    @rtype     : object

    >>> snp.from_string('AA')
    ('A', 'A')
    >>> snp.from_string('AB')
    ('A', 'B')
    >>> snp.from_string('BA')
    ('A', 'B')
    >>> snp.from_string(' A')
    (None, 'A')
    >>> snp.from_string('A ')
    (None, 'A')
    >>> snp.from_string('  ')
    (None, None)
    >>> snp.from_string('')
    (None, None)

    >>> hapmap.from_string('AA')
    ('A', 'A')
    >>> hapmap.from_string('AB')
    ('A', 'B')
    >>> hapmap.from_string('BA')
    ('A', 'B')
    >>> hapmap.from_string('NA')
    (None, 'A')
    >>> hapmap.from_string('AN')
    (None, 'A')
    >>> hapmap.from_string('NN')
    (None, None)

    >>> marker.from_string('A/A')
    ('A', 'A')
    >>> marker.from_string('A/B')
    ('A', 'B')
    >>> marker.from_string('B/A')
    ('A', 'B')
    >>> marker.from_string(' /A')
    (None, 'A')
    >>> marker.from_string('/A')
    (None, 'A')
    >>> marker.from_string('A/ ')
    (None, 'A')
    >>> marker.from_string('A/')
    (None, 'A')
    >>> marker.from_string(' / ')
    (None, None)
    >>> marker.from_string('/')
    (None, None)
    >>> marker.from_string('/ ')
    (None, None)
    >>> marker.from_string(' /')
    (None, None)
    >>> marker.from_string('')
    (None, None)
    """
        strcache = self.strcache
        if geno in strcache:
            return strcache[geno]
        if geno in self.missing_geno_strs:
            rep = self.strcache[geno] = None, None
            return rep
        if self.delimiter:
            alleles = geno.split(self.delimiter)
        else:
            alleles = geno
        if len(alleles) != 2:
            raise ValueError('Invalid genotype: %s' % geno)
        rep = self.strcache[intern(geno)] = tuple(sorted(self.allelestr.
            setdefault(a, a) for a in alleles))
        return rep

    def from_strings(self, genos):
        """
    Transform a sequence of genotype strings to internal format

    @param genos: sequence of genotype strings
    @type  genos: sequence of str
    @return     : sequence of genotype in internal format
    @rtype      : sequence of objects

    >>> snp.from_strings(['AA','AB','BA',' A','A ','  ',''])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None), (None, None)]
    >>> hapmap.from_strings(['AA','AB','BA','NA','AN','NN'])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None)]
    >>> marker.from_strings(['A/A','A/B','B/A',' /A','A/ ',' / ',''])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None), (None, None)]
    """
        try:
            return list(imap(getitem, repeat(self.strcache), genos))
        except KeyError:
            return map(self.from_string, genos)


<mask token>


def get_genorepr(reprname):
    """
  Retrieve the supported genotype representation. Otherwise raises an ValueError exception

  @param reprname: internal genotype representation
  @type  reprname: str
  @return        : supported genotype representation
  @rtype         : genotype representation object
  """
    reprs = {'snp': snp, 'isnp': isnp, 'hapmap': hapmap, 'marker': marker}
    if not reprname:
        reprname = 'snp'
    try:
        return reprs[reprname]
    except KeyError:
        raise ValueError('Unknown genotype representation: %s' % reprname)


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


<mask token>

__abstract__ = 'Genotype representation parsers for text file input/output'
__copyright__ = (
    'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
    )
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
from operator import getitem
from itertools import imap, repeat


class Nothing(object):
    pass


class UnphasedMarkerRepresentation(object):
    """
  Generic unphased marker representation where the genotype representation
  and internal representation are the same.
  """

    def __init__(self, missing_geno_str=Nothing, missing_geno_strs=(),
        missing_allele_str='', missing_allele_strs=(), delimiter='/'):
        """
    Construct a new UnphasedMarkerRepresentation

    This class represents bidirectional mappings of genotypes between
    strings and Python objects.  The object representation of a genotype is
    a tuple of two alleles, with the missing genotype being None or any
    other object that evaluates to False.  Given this representation,
    alleles need not be known in advance.  The "internal representation" is
    the same as the Python object representation (for an example of a non-
    trivial internal representation see UnphasedMarkerRepresentation
    below).

    @param    missing_geno_str: canonical missing genotype output string representation, optional
                                and defaults to Nothing
    @type     missing_geno_str: str
    @param   missing_geno_strs: missing genotype input strings
    @type    missing_geno_strs: sequence
    @param  missing_allele_str: canonical missing allele output string representation, default is ''
                                and defaults to an empty string
    @type   missing_allele_str: str
    @param missing_allele_strs: missing allele input strings
    @type  missing_allele_strs: sequence
    @param           delimiter: allele delimiter for genotypes, defaults is '/'
    @type            delimiter: str
    """
        self.missing_geno_str = missing_geno_str
        self.missing_geno_strs = missing_geno_strs
        self.missing_allele_str = missing_allele_str
        self.missing_allele_strs = missing_allele_strs
        self.delimiter = delimiter
        self.allelerep = {None: self.missing_allele_str}
        self.allelestr = dict((m, None) for m in missing_allele_strs)
        self.missing = None
        self.strcache = {}

    def to_string(self, rep):
        """
    Transform a genotype in internal format to a genotype string

    @param rep: genotype in internal format
    @type  rep: object
    @return   : genotype in string format
    @rtype    : str

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> snp.to_string( model['A','A'] )
    'AA'
    >>> snp.to_string( model[None, 'A'] )
    ' A'
    >>> snp.to_string( model['A', None] )
    ' A'
    >>> snp.to_string( model[None,None])
    '  '
    >>> hapmap.to_string( model['A','A'] )
    'AA'
    >>> hapmap.to_string( model[None, 'A'] )
    'NA'
    >>> hapmap.to_string( model['A', None] )
    'NA'
    >>> hapmap.to_string( model[None,None])
    'NN'
    >>> marker.to_string( model['A','A'] )
    'A/A'
    >>> marker.to_string( model[None, 'A'] )
    '/A'
    >>> marker.to_string( model['A', None] )
    '/A'
    >>> marker.to_string( model[None,None])
    ''
    """
        rep = rep.alleles()
        strcache = self.strcache
        if rep in strcache:
            return strcache[rep]
        if rep == (None, None):
            if self.missing_geno_str is not Nothing:
                return self.missing_geno_str
        alleles = [self.allelerep.setdefault(a, a) for a in rep]
        if not self.delimiter:
            for a in alleles:
                if len(a) > 1:
                    raise ValueError('Invalid genotype representation')
        gstr = strcache[rep] = self.delimiter.join(alleles)
        return gstr

    def to_string_from_alleles(self, rep):
        """
    Transform a genotype tuple to a genotype string

    @param rep: genotype in tuple format
    @type  rep: object
    @return   : genotype in string format
    @rtype    : str

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> snp.to_string_from_alleles( ('A','A') )
    'AA'
    >>> snp.to_string_from_alleles( (None, 'A') )
    ' A'
    >>> snp.to_string_from_alleles( ('A', None) )
    'A '
    >>> snp.to_string_from_alleles( (None,None))
    '  '
    >>> hapmap.to_string_from_alleles( ('A','A') )
    'AA'
    >>> hapmap.to_string_from_alleles( (None, 'A') )
    'NA'
    >>> hapmap.to_string_from_alleles( ('A', None) )
    'AN'
    >>> hapmap.to_string_from_alleles( (None,None))
    'NN'
    >>> marker.to_string_from_alleles( ('A','A') )
    'A/A'
    >>> marker.to_string_from_alleles( (None, 'A') )
    '/A'
    >>> marker.to_string_from_alleles( ('A', None) )
    'A/'
    >>> marker.to_string_from_alleles( (None,None))
    ''
    """
        strcache = self.strcache
        if rep in strcache:
            return strcache[rep]
        if rep == (None, None):
            if self.missing_geno_str is not Nothing:
                return self.missing_geno_str
        alleles = [self.allelerep.setdefault(a, a) for a in rep]
        if not self.delimiter:
            for a in alleles:
                if len(a) > 1:
                    raise ValueError('Invalid genotype representation')
        gstr = strcache[rep] = self.delimiter.join(alleles)
        return gstr

    def to_strings(self, reps):
        """
    Transform a sequence of genotypes in internal format to a genotype strings

    @param reps: genotypes in internal format
    @type  reps: sequence
    @return    : genotypes in string format
    @rtype     : sequence

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> genos = [ model[g] for g in [('A','A'),(None,'A'),(None,None)] ]
    >>> snp.to_strings(genos)
    ['AA', ' A', '  ']
    >>> hapmap.to_strings(genos)
    ['AA', 'NA', 'NN']
    >>> marker.to_strings(genos)
    ['A/A', '/A', '']
    """
        try:
            strcache = self.strcache
            return [strcache[r.alleles()] for r in reps]
        except KeyError:
            return map(self.to_string, reps)

    def from_string(self, geno):
        """
    Transform a genotype string to internal format

    @param geno: genotype string
    @type  geno: str
    @return    : genotype in internal format
    @rtype     : object

    >>> snp.from_string('AA')
    ('A', 'A')
    >>> snp.from_string('AB')
    ('A', 'B')
    >>> snp.from_string('BA')
    ('A', 'B')
    >>> snp.from_string(' A')
    (None, 'A')
    >>> snp.from_string('A ')
    (None, 'A')
    >>> snp.from_string('  ')
    (None, None)
    >>> snp.from_string('')
    (None, None)

    >>> hapmap.from_string('AA')
    ('A', 'A')
    >>> hapmap.from_string('AB')
    ('A', 'B')
    >>> hapmap.from_string('BA')
    ('A', 'B')
    >>> hapmap.from_string('NA')
    (None, 'A')
    >>> hapmap.from_string('AN')
    (None, 'A')
    >>> hapmap.from_string('NN')
    (None, None)

    >>> marker.from_string('A/A')
    ('A', 'A')
    >>> marker.from_string('A/B')
    ('A', 'B')
    >>> marker.from_string('B/A')
    ('A', 'B')
    >>> marker.from_string(' /A')
    (None, 'A')
    >>> marker.from_string('/A')
    (None, 'A')
    >>> marker.from_string('A/ ')
    (None, 'A')
    >>> marker.from_string('A/')
    (None, 'A')
    >>> marker.from_string(' / ')
    (None, None)
    >>> marker.from_string('/')
    (None, None)
    >>> marker.from_string('/ ')
    (None, None)
    >>> marker.from_string(' /')
    (None, None)
    >>> marker.from_string('')
    (None, None)
    """
        strcache = self.strcache
        if geno in strcache:
            return strcache[geno]
        if geno in self.missing_geno_strs:
            rep = self.strcache[geno] = None, None
            return rep
        if self.delimiter:
            alleles = geno.split(self.delimiter)
        else:
            alleles = geno
        if len(alleles) != 2:
            raise ValueError('Invalid genotype: %s' % geno)
        rep = self.strcache[intern(geno)] = tuple(sorted(self.allelestr.
            setdefault(a, a) for a in alleles))
        return rep

    def from_strings(self, genos):
        """
    Transform a sequence of genotype strings to internal format

    @param genos: sequence of genotype strings
    @type  genos: sequence of str
    @return     : sequence of genotype in internal format
    @rtype      : sequence of objects

    >>> snp.from_strings(['AA','AB','BA',' A','A ','  ',''])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None), (None, None)]
    >>> hapmap.from_strings(['AA','AB','BA','NA','AN','NN'])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None)]
    >>> marker.from_strings(['A/A','A/B','B/A',' /A','A/ ',' / ',''])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None), (None, None)]
    """
        try:
            return list(imap(getitem, repeat(self.strcache), genos))
        except KeyError:
            return map(self.from_string, genos)


snp = UnphasedMarkerRepresentation(delimiter='', missing_geno_str='  ',
    missing_geno_strs=['', '  '], missing_allele_str=' ',
    missing_allele_strs=['', ' '])
isnp = UnphasedMarkerRepresentation(delimiter='', missing_geno_str='--',
    missing_geno_strs=['', '--'], missing_allele_str='-',
    missing_allele_strs=['-'])
hapmap = UnphasedMarkerRepresentation(delimiter='', missing_geno_str='NN',
    missing_geno_strs=['', 'NN'], missing_allele_str='N',
    missing_allele_strs=['N'])
marker = UnphasedMarkerRepresentation(delimiter='/', missing_geno_str='',
    missing_geno_strs=['', '/'], missing_allele_str='', missing_allele_strs
    =['', ' '])


def get_genorepr(reprname):
    """
  Retrieve the supported genotype representation. Otherwise raises an ValueError exception

  @param reprname: internal genotype representation
  @type  reprname: str
  @return        : supported genotype representation
  @rtype         : genotype representation object
  """
    reprs = {'snp': snp, 'isnp': isnp, 'hapmap': hapmap, 'marker': marker}
    if not reprname:
        reprname = 'snp'
    try:
        return reprs[reprname]
    except KeyError:
        raise ValueError('Unknown genotype representation: %s' % reprname)


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


if __name__ == '__main__':
    main()

# -*- coding: utf-8 -*-

__abstract__  = 'Genotype representation parsers for text file input/output'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__   = 'See GLU license for terms by running: glu license'
__revision__  = '$Id$'

from   operator                   import getitem
from   itertools                  import imap, repeat


class Nothing(object): pass

# Glossary of terms:
#   genotype tuple  = tuple of two alleles or None if missing.
#   internal rep    = opaque object representing a genotype,
#                     evaluates to False iff missing
#   genotype string = string representation
#   packed          = random access sequence of internal genotype reps


class UnphasedMarkerRepresentation(object):
  '''
  Generic unphased marker representation where the genotype representation
  and internal representation are the same.
  '''

  def __init__(self, missing_geno_str=Nothing, missing_geno_strs=(),
                     missing_allele_str='',    missing_allele_strs=(),
                     delimiter='/'):
    '''
    Construct a new UnphasedMarkerRepresentation

    This class represents bidirectional mappings of genotypes between
    strings and Python objects.  The object representation of a genotype is
    a tuple of two alleles, with the missing genotype being None or any
    other object that evaluates to False.  Given this representation,
    alleles need not be known in advance.  The "internal representation" is
    the same as the Python object representation (for an example of a non-
    trivial internal representation see UnphasedMarkerRepresentation
    below).

    @param    missing_geno_str: canonical missing genotype output string representation, optional
                                and defaults to Nothing
    @type     missing_geno_str: str
    @param   missing_geno_strs: missing genotype input strings
    @type    missing_geno_strs: sequence
    @param  missing_allele_str: canonical missing allele output string representation, default is ''
                                and defaults to an empty string
    @type   missing_allele_str: str
    @param missing_allele_strs: missing allele input strings
    @type  missing_allele_strs: sequence
    @param           delimiter: allele delimiter for genotypes, defaults is '/'
    @type            delimiter: str
    '''
    self.missing_geno_str    = missing_geno_str
    self.missing_geno_strs   = missing_geno_strs
    self.missing_allele_str  = missing_allele_str
    self.missing_allele_strs = missing_allele_strs
    self.delimiter           = delimiter

    self.allelerep  = {None:self.missing_allele_str}
    self.allelestr  = dict( (m,None) for m in missing_allele_strs )
    self.missing    = None
    self.strcache   = {}

  def to_string(self, rep):
    '''
    Transform a genotype in internal format to a genotype string

    @param rep: genotype in internal format
    @type  rep: object
    @return   : genotype in string format
    @rtype    : str

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> snp.to_string( model['A','A'] )
    'AA'
    >>> snp.to_string( model[None, 'A'] )
    ' A'
    >>> snp.to_string( model['A', None] )
    ' A'
    >>> snp.to_string( model[None,None])
    '  '
    >>> hapmap.to_string( model['A','A'] )
    'AA'
    >>> hapmap.to_string( model[None, 'A'] )
    'NA'
    >>> hapmap.to_string( model['A', None] )
    'NA'
    >>> hapmap.to_string( model[None,None])
    'NN'
    >>> marker.to_string( model['A','A'] )
    'A/A'
    >>> marker.to_string( model[None, 'A'] )
    '/A'
    >>> marker.to_string( model['A', None] )
    '/A'
    >>> marker.to_string( model[None,None])
    ''
    '''
    # Macro-optimized
    #return self.to_string_from_alleles(rep.alleles())
    rep = rep.alleles()
    strcache = self.strcache
    if rep in strcache:
      return strcache[rep]

    if rep == (None,None):
      if self.missing_geno_str is not Nothing:
        return self.missing_geno_str

    alleles = [ self.allelerep.setdefault(a,a) for a in rep ]

    if not self.delimiter:
      for a in alleles:
        if len(a) > 1:
         raise ValueError('Invalid genotype representation')

    gstr = strcache[rep] = self.delimiter.join(alleles)
    return gstr

  def to_string_from_alleles(self,rep):
    '''
    Transform a genotype tuple to a genotype string

    @param rep: genotype in tuple format
    @type  rep: object
    @return   : genotype in string format
    @rtype    : str

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> snp.to_string_from_alleles( ('A','A') )
    'AA'
    >>> snp.to_string_from_alleles( (None, 'A') )
    ' A'
    >>> snp.to_string_from_alleles( ('A', None) )
    'A '
    >>> snp.to_string_from_alleles( (None,None))
    '  '
    >>> hapmap.to_string_from_alleles( ('A','A') )
    'AA'
    >>> hapmap.to_string_from_alleles( (None, 'A') )
    'NA'
    >>> hapmap.to_string_from_alleles( ('A', None) )
    'AN'
    >>> hapmap.to_string_from_alleles( (None,None))
    'NN'
    >>> marker.to_string_from_alleles( ('A','A') )
    'A/A'
    >>> marker.to_string_from_alleles( (None, 'A') )
    '/A'
    >>> marker.to_string_from_alleles( ('A', None) )
    'A/'
    >>> marker.to_string_from_alleles( (None,None))
    ''
    '''
    strcache = self.strcache
    if rep in strcache:
      return strcache[rep]

    if rep == (None,None):
      if self.missing_geno_str is not Nothing:
        return self.missing_geno_str

    alleles = [ self.allelerep.setdefault(a,a) for a in rep ]

    if not self.delimiter:
      for a in alleles:
        if len(a) > 1:
         raise ValueError('Invalid genotype representation')

    gstr = strcache[rep] = self.delimiter.join(alleles)
    return gstr

  def to_strings(self,reps):
    '''
    Transform a sequence of genotypes in internal format to a genotype strings

    @param reps: genotypes in internal format
    @type  reps: sequence
    @return    : genotypes in string format
    @rtype     : sequence

    >>> from glu.lib.genolib.genoarray import build_model
    >>> model=build_model('AG',allow_hemizygote=True)
    >>> genos = [ model[g] for g in [('A','A'),(None,'A'),(None,None)] ]
    >>> snp.to_strings(genos)
    ['AA', ' A', '  ']
    >>> hapmap.to_strings(genos)
    ['AA', 'NA', 'NN']
    >>> marker.to_strings(genos)
    ['A/A', '/A', '']
    '''
    try:
      strcache = self.strcache
      return [ strcache[r.alleles()] for r in reps ]
    except KeyError:
      return map(self.to_string, reps)

  def from_string(self, geno):
    '''
    Transform a genotype string to internal format

    @param geno: genotype string
    @type  geno: str
    @return    : genotype in internal format
    @rtype     : object

    >>> snp.from_string('AA')
    ('A', 'A')
    >>> snp.from_string('AB')
    ('A', 'B')
    >>> snp.from_string('BA')
    ('A', 'B')
    >>> snp.from_string(' A')
    (None, 'A')
    >>> snp.from_string('A ')
    (None, 'A')
    >>> snp.from_string('  ')
    (None, None)
    >>> snp.from_string('')
    (None, None)

    >>> hapmap.from_string('AA')
    ('A', 'A')
    >>> hapmap.from_string('AB')
    ('A', 'B')
    >>> hapmap.from_string('BA')
    ('A', 'B')
    >>> hapmap.from_string('NA')
    (None, 'A')
    >>> hapmap.from_string('AN')
    (None, 'A')
    >>> hapmap.from_string('NN')
    (None, None)

    >>> marker.from_string('A/A')
    ('A', 'A')
    >>> marker.from_string('A/B')
    ('A', 'B')
    >>> marker.from_string('B/A')
    ('A', 'B')
    >>> marker.from_string(' /A')
    (None, 'A')
    >>> marker.from_string('/A')
    (None, 'A')
    >>> marker.from_string('A/ ')
    (None, 'A')
    >>> marker.from_string('A/')
    (None, 'A')
    >>> marker.from_string(' / ')
    (None, None)
    >>> marker.from_string('/')
    (None, None)
    >>> marker.from_string('/ ')
    (None, None)
    >>> marker.from_string(' /')
    (None, None)
    >>> marker.from_string('')
    (None, None)
    '''
    strcache = self.strcache
    if geno in strcache:
      return strcache[geno]

    if geno in self.missing_geno_strs:
      rep = self.strcache[geno] = (None,None)
      return rep

    if self.delimiter:
      alleles = geno.split(self.delimiter)
    else:
      alleles = geno

    if len(alleles) != 2:
      raise ValueError('Invalid genotype: %s' % geno)

    rep = self.strcache[intern(geno)] = \
          tuple(sorted(self.allelestr.setdefault(a,a) for a in alleles))

    return rep

  def from_strings(self,genos):
    '''
    Transform a sequence of genotype strings to internal format

    @param genos: sequence of genotype strings
    @type  genos: sequence of str
    @return     : sequence of genotype in internal format
    @rtype      : sequence of objects

    >>> snp.from_strings(['AA','AB','BA',' A','A ','  ',''])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None), (None, None)]
    >>> hapmap.from_strings(['AA','AB','BA','NA','AN','NN'])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None)]
    >>> marker.from_strings(['A/A','A/B','B/A',' /A','A/ ',' / ',''])
    [('A', 'A'), ('A', 'B'), ('A', 'B'), (None, 'A'), (None, 'A'), (None, None), (None, None)]
    '''
    try:
      return list(imap(getitem, repeat(self.strcache), genos))
    except KeyError:
      return map(self.from_string, genos)


# GLU native SNP format
snp    = UnphasedMarkerRepresentation(delimiter='', missing_geno_str='  ',missing_geno_strs=['','  '],
                                      missing_allele_str=' ',missing_allele_strs=['',' '])
# Illumina SNP data from BeadStudio
isnp   = UnphasedMarkerRepresentation(delimiter='', missing_geno_str='--',missing_geno_strs=['','--'],
                                      missing_allele_str='-',missing_allele_strs=['-'])

# HapMap SNP format
hapmap = UnphasedMarkerRepresentation(delimiter='',missing_geno_str='NN',missing_geno_strs=['','NN'],
                                      missing_allele_str='N',missing_allele_strs=['N'],)

# Delimited marker format using a slash
marker = UnphasedMarkerRepresentation(delimiter='/',missing_geno_str='',missing_geno_strs=['','/'],
                                      missing_allele_str='',missing_allele_strs=['',' '])


def get_genorepr(reprname):
  '''
  Retrieve the supported genotype representation. Otherwise raises an ValueError exception

  @param reprname: internal genotype representation
  @type  reprname: str
  @return        : supported genotype representation
  @rtype         : genotype representation object
  '''

  reprs = { 'snp'    : snp,
            'isnp'   : isnp,
            'hapmap' : hapmap,
            'marker' : marker }

  if not reprname:
    reprname = 'snp'

  try:
    return reprs[reprname]
  except KeyError:
    raise ValueError('Unknown genotype representation: %s' % reprname)


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


if __name__ == '__main__':
  main()
