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Sourcecode: python-biopython version File versions  Download package


# Decode elements from a Std/Martel parsed XML stream

import string
from Bio.Parsers.spark import GenericScanner, GenericParser

def unescape_C(s):
    result = []
    for i in range(len(s)):
        if s[i] != "\\":
        c = s[i+1:i+2]
        if c == "x":
            x = s[i+2:i+4]
            if len(x) != 2:
                raise ValueError("invalid \\x escape")
            i = int(x, 16)
        if c in "01234567":
            x = s[i+1:i+4]
            # \octals don't do a length assertion check
            i = int(x, 8)
    return "".join(result)

def join_english(fields):
    if not fields:
        return ""
    s = fields[0]
    for field in fields[1:]:
        if s[-1:] == "-" and s[-3:-2] == "-":
            s = s + field
        if s.find(" ") == -1 and field.find(" ") == -1:
            s = s + field
        s = s + " " + field
    return (" ".join(s.split())).strip()

def chomp(s, c):
    if s[-1:] == c:
        return s[:-1]
    return s

def lchomp(s, c):
    if s[:1] == c:
        return s[1:]
    return s
def chompchomp(s, c):
    if s[:1] == c and s[-1:] == c:
        return s[1:-1]
    return s

def fixspaces(s):
    # s.split breaks down to a list of words
    # " ".join puts them together
    # strip removes leading and trailing spaces
    return " ".join(s.split()).strip()

def join_fixspaces(lines):
    return " ".join((" ".join(lines)).split()).strip()

def tr(s, frm, to):
    table = string.maketrans(frm, to)
    return string.translate(s, table)

def safe_int(s):
    """converts to int if the number is small, long if it's large"""
        return int(s)
    except ValueError:
        return long(s)

decode_functions = {
    "chomp": (chomp, str, str),
    "chompchomp": (chompchomp, str, str),
    "chop": (lambda s: s[:-1], str, str),
    "chopchop": (lambda s: s[1:-1], str, str),
    "fixspaces": (fixspaces, str, str),
    "lchomp": (lchomp, str, str),
    "lchop": (lambda s: s[1:], str, str),
    "lower": (lambda s: s.lower(), str, str),
    "lstrip": (lambda s: s.lstrip(), str, str),
    "replace": (lambda s, old, new: s.replace(old, new), str, str),
    "rstrip": (lambda s: s.rstrip(), str, str),
    "str": (str, str, str),
    "strip": (lambda s: s.strip(), str, str),
    "tr": (tr, str, str),
    "unescape.c": (unescape_C, str, str),
    "unescape.doublequote": (lambda s: s.replace('""', '"'), str, str),
    "unescape.singlequote": (lambda s: s.replace("''", "'"), str, str),
    "upper": (lambda s: s.upper(), str, str),

    # List operations
    "join": (lambda lst, s = " ": s.join(lst), list, str),
    "join.english": (join_english, list, str),

    # Integer operations
    "int": (safe_int, [float, str, int], int),
    "int.comma": (lambda s: safe_int(s.replace(",", "")),
                  [float, str, int], int),
    "hex": (hex, str, int),
    "oct": (oct, str, int),
    "add": ((lambda i, j: i+j), int, int),

    # Float operations
    "float": (float, (float, str, int), float),

def _fixup_defs():
    # Normalize so the 2nd and 3rd terms are tuples
    for k, v in decode_functions.items():
        f, in_types, out_types = v
        if isinstance(in_types, type([])):
            in_types = tuple(in_types)
        elif not isinstance(in_types, type( () )):
            in_types = (in_types,)

        if isinstance(out_types, type([])):
            out_types = tuple(out_types)
        elif not isinstance(out_types, type( () )):
            out_types = (out_types,)

        decode_functions[k] = (f, in_types, out_types)

class Token:
    def __init__(self, type):
        self.type = type
    def __cmp__(self, other):
        return cmp(self.type, other)
    def __repr__(self):
        return "Token(%r)" % (self.type,)

class ValueToken(Token):
    def __init__(self, type, val):
        Token.__init__(self, type)
        self.val = val
    def __cmp__(self, other):
        return cmp(self.type, other)
    def __repr__(self):
        return "%s(%r)" % (self.__class__.__name__, self.val)
    def __str__(self):
        return str(self.val)

class Integer(ValueToken):
    def __init__(self, val):
        ValueToken.__init__(self, "integer", val)

class Float(ValueToken):
    def __init__(self, val):
        ValueToken.__init__(self, "float", val)

class String(ValueToken):
    def __init__(self, val):
        ValueToken.__init__(self, "string", val)

class FunctionName(ValueToken):
    def __init__(self, val):
        ValueToken.__init__(self, "functionname", val)

class DecodeScanner(GenericScanner):
    def __init__(self):
    def tokenize(self, input):
        self.rv = []
        GenericScanner.tokenize(self, input)
        return self.rv

    def t_functionname(self, input):
        r" \w+(\.\w+)*"

    def t_pipe(self, input):
        r" \| "
    def t_open_paren(self, input):
        r" \( "

    def t_close_paren(self, input):
        r" \) "

    def t_comma(self, input):
        r" , "

    def t_whitespace(self, input):
        r" \s+ "

    def t_string(self, input):
        r""" "([^"\\]+|\\.)*"|'([^'\\]+|\\.)*' """
        # "'  # emacs cruft
        s = input[1:-1]
        s = unescape_C(s)

    def t_float(self, input):
        r""" [+-]?((\d+(\.\d*)?)|\.\d+)([eE][+-]?[0-9]+)? """
        # See if this is an integer
        except ValueError:

class Function:
    def __init__(self, name, args = ()):
        self.name = name
        self.args = args
    def __str__(self):
        args = self.args
        if not args:
            s = ""
            s = str(args)[1:-1]
        return "%s(x, %s)" % (self.name, s)
    __repr__ = __str__

class DecodeParser(GenericParser):
    def __init__(self, start = "expression"):
        GenericParser.__init__(self, start)
        self.begin_pos = 0

    def p_expression(self, args):
        expression ::= term
        expression ::= term pipe expression
        if len(args) == 1:
            return [args[0]]
        return [args[0]] + args[2]

    def p_term(self, args):
        term ::= functionname
        term ::= functionname open_paren args close_paren
        if len(args) == 1:
            return Function(args[0].val)
        return Function(args[0].val, tuple([x.val for x in args[2]]))

    def p_args(self, args):
        args ::= arg
        args ::= arg comma args
        if len(args) == 1:
            return [args[0]]
        return [args[0]] + args[2]

    def p_arg(self, args):
        arg ::= string
        arg ::= integer
        arg ::= float
        return args[0]
def scan(input):
    scanner = DecodeScanner()
    return scanner.tokenize(input)

def parse(tokens):
    parser = DecodeParser()
    return parser.parse(tokens)

_decoder_cache = {}

class FunctionCall:
    def __init__(self, f, args):
        self.f = f
        self.args = args
    def __call__(self, x):
        return self.f(x, *self.args)

class FunctionCallChain:
    def __init__(self, inner_f, f, args):
        self.inner_f = inner_f
        self.f = f
        self.args = args
    def __call__(self, x):
        return self.f(self.inner_f(x), *self.args)

#### I don't think this is the right way to do things
##class CheckTypes:
##    def __init__(self, f, call_types, return_types):
##        self.f = f
##        self.call_types = call_types
##        self.return_types = return_types
##    def __call__(self, x):
##        if self.call_types is not None:
##            for T in self.call_types:
##                if isinstance(x, T):
##                    break
##            else:
##                raise TypeError(
##                    "Call value %s of type %s, expecting one of %s" %
##                    (x, type(x).__name__,
##                     [T.name for T in self.call_types]))
##        y = self.f(x)

##        if not self.return_types:
##            return y
##        for T in self.return_types:
##            if isinstance(y, T):
##                return y
##        raise TypeError("Return value %s of type %s, expecting one of %s" %
##                        (y, type(y).__name__,
##                         [T.name for T in self.return_types]))

def make_decoder(s):
        return _decoder_cache[s]
    except KeyError:
    functions = parse(scan(s))
    f = functions[0]
    fc = decode_functions[f.name][0]
    args = f.args
    if args:
        fc = FunctionCall(fc, args)
    for f in functions[1:]:
        fc = FunctionCallChain(fc, decode_functions[f.name][0], f.args)
    _decoder_cache[s] = fc
    return fc

def _verify_subtypes(subset, total, old_name, new_name):
    for x in subset:
        if x not in total:
            raise TypeError("%s can produce a %r value not accepted by %s" %
                            (old_name, x.__name__, new_name))

_typechecked_decoder_cache = {}
def make_typechecked_decoder(s, input_types = None, output_types = None):
    cache_lookup = (s, input_types, output_types)
        return _typechecked_decoder_cache[cache_lookup]
    except KeyError:
    if input_types is not None and not isinstance(input_types, type( () )):
        input_types = (input_types,)
    if output_types is not None and not isinstance(output_types, type( () )):
        output_types = (output_types,)

    functions = parse(scan(s))

    # Make sure the input type(s) are allowed
    f = functions[0]
    fc, in_types, out_types = decode_functions[f.name]
    if input_types is not None:
        for x in input_types:
            if x not in in_types:
                raise TypeError(
                    "the input type includes %r which isn't supported by %s" %
                    (x.__name__, f.name))

    # Do the composition
    old_name = f.name
    input_types = out_types
    args = functions[0].args
    if args:
        fc = FunctionCall(fc, args)
    for f in functions[1:]:
        transform_func, in_types, out_types = decode_functions[f.name]
        _verify_subtypes(input_types, in_types, old_name, f.name)
        old_name = f.name
        input_types = out_types
        fc = FunctionCallChain(fc, transform_func, f.args)

    if output_types is not None:
        _verify_subtypes(input_types, output_types, old_name, "the output")
    _typechecked_decoder_cache[cache_lookup] = fc
    return fc

def test():
    assert make_decoder("chop")("Andrew") == "Andre"
    assert make_decoder("int")("9") == 9
    assert make_decoder('join(" ")')(["Andrew", "Dalke"]) == \
                                          "Andrew Dalke"
    assert make_decoder('chomp("|")')("|test|") == "|test"
    assert make_decoder('chomp("|")')("|test") == "|test"
    assert make_decoder('chomp("A")|chop')("BA") == ""
    assert make_decoder('chomp("A")|chop')("AB") == "A"
    assert make_decoder('chop|chomp("A")')("AB") == ""
    assert make_decoder('chop|chomp("A")')("BA") == "B"
    assert make_decoder('add(5)')(2) == 7
    assert make_decoder('add(-2)')(5) == 3
if __name__ == "__main__":

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