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# Copyright 1999 by Jeffrey Chang.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Module to work with enzyme.dat file (DEPRECATED).

This module provides code to work with the enzyme.dat file from
Enzyme (OBSOLETE as of Biopython version 1.50).

The functionality of Bio.Enzyme has moved to Bio.ExPASy.ExPASy;
please use that module instead of Bio.Enzyme. Bio.Enzyme is now
deprecated and will be removed in a future release of Biopython.

import warnings
import Bio
warnings.warn("Bio.Enzyme is deprecated, and will be removed in a"\
              " future release of Biopython. Most of the functionality "
              " is now provided by Bio.ExPASy.Enzyme.  If you want to "
              " continue to use Bio.Enzyme, please get in contact "
              " via the mailing lists to avoid its permanent removal from"\
              " Biopython.", Bio.BiopythonDeprecationWarning)

from Bio import File
from Bio.ParserSupport import *

00029 class _Scanner:
    """Scans Enzyme data (PRIVATE).

    Tested with:
    Release 33

00036     def feed(self, handle, consumer):
        """feed(self, handle, consumer)

        Feed in Enzyme data for scanning.  handle is a file-like object
        that contains keyword information.  consumer is a Consumer
        object that will receive events as the report is scanned.

        if isinstance(handle, File.UndoHandle):
            uhandle = handle
            uhandle = File.UndoHandle(handle)

        while not is_blank_line(uhandle.peekline()):   # Am I done yet?
            self._scan_record(uhandle, consumer)

    def _scan_record(self, uhandle, consumer):
        # The first record is just copyright information embedded in
        # comments.  Check to see if I'm at the first record.  If so,
        # then just scan the comments and the terminator.
        line = uhandle.peekline()
        if line[:2] == 'CC':
            self._scan_cc(uhandle, consumer)
            self._scan_terminator(uhandle, consumer)
            for fn in self._scan_fns:
                fn(self, uhandle, consumer)

    def _scan_line(self, line_type, uhandle, event_fn,
                   exactly_one=None, one_or_more=None, any_number=None,
        # Callers must set exactly one of exactly_one, one_or_more, or
        # any_number to a true value.  I do not explicitly check to
        # make sure this function is called correctly.
        # This does not guarantee any parameter safety, but I
        # like the readability.  The other strategy I tried was have
        # parameters min_lines, max_lines.
        if exactly_one or one_or_more:
            read_and_call(uhandle, event_fn, start=line_type)
        if one_or_more or any_number:
            while 1:
                if not attempt_read_and_call(uhandle, event_fn,
        if up_to_one:
            attempt_read_and_call(uhandle, event_fn, start=line_type)

    def _scan_id(self, uhandle, consumer):
        self._scan_line('ID', uhandle, consumer.identification, exactly_one=1)

    def _scan_de(self, uhandle, consumer):
        self._scan_line('DE', uhandle, consumer.description, one_or_more=1)
    def _scan_an(self, uhandle, consumer):
        self._scan_line('AN', uhandle, consumer.alternate_name, any_number=1)
    def _scan_ca(self, uhandle, consumer):
        self._scan_line('CA', uhandle, consumer.catalytic_activity,
    def _scan_cf(self, uhandle, consumer):
        self._scan_line('CF', uhandle, consumer.cofactor, any_number=1)

    def _scan_cc(self, uhandle, consumer):
        self._scan_line('CC', uhandle, consumer.comment, any_number=1)
    def _scan_di(self, uhandle, consumer):
        self._scan_line('DI', uhandle, consumer.disease, any_number=1)
    def _scan_pr(self, uhandle, consumer):
        self._scan_line('PR', uhandle, consumer.prosite_reference,
    def _scan_dr(self, uhandle, consumer):
        self._scan_line('DR', uhandle, consumer.databank_reference,

    def _scan_terminator(self, uhandle, consumer):
        self._scan_line('//', uhandle, consumer.terminator, exactly_one=1)
    _scan_fns = [
00132 class DataRecord:
    def __init__(self,tr_code='',sw_code=''):
        self.tr_code = tr_code
        self.sw_code = sw_code
    def __str__(self):
        return self.tr_code + ", " + self.sw_code
00140 class EnzymeRecord:
    def __init__(self):
        self.ID = ''
        self.DE = []
        self.AN = []
        self.CA = ''
        self.CF = []
        self.CC = []   # one comment per line
        self.DI = []
        self.PR = []
        self.DR = []
    def __repr__(self):
        if self.ID:
            if self.DE:
                return "%s (%s, %s)" % (self.__class__.__name__, 
                                        self.ID, self.DE[0])
                return "%s (%s)" % (self.__class__.__name__, 
            return "%s ( )" % (self.__class__.__name__)
    def __str__(self):
        output = "ID: " + self.ID
        output += " DE: " + repr(self.DE)
        output += " AN: " + repr(self.AN)
        output += " CA: '" + self.CA + "'"
        output += " CF: " + repr(self.CF)
        output += " CC: " + repr(self.CC)
        output += " DI: " + repr(self.DI)
        output += " PR: " + repr(self.PR)
        output += " DR: %d Records" % len(self.DR)
        return output
00176 class RecordParser(AbstractParser):
    def __init__(self):
        self._scanner = _Scanner()
        self._consumer = _RecordConsumer()

    def parse(self, handle):
        if isinstance(handle, File.UndoHandle):
            uhandle = handle
            uhandle = File.UndoHandle(handle)
            self._scanner.feed(uhandle, self._consumer)
        return self._consumer.enzyme_record

00189 class Iterator:
    def __init__(self, handle, parser=None):
        self._uhandle = File.UndoHandle(handle)

    def next(self):
        self._parser = RecordParser()
        lines = []
        while True:
            line = self._uhandle.readline()
            if not line: break
            if line[:2] == '//':
        if not lines:
            return None
        data = ''.join(lines)
        if self._parser is not None:
            return self._parser.parse(File.StringHandle(data))
        return data

    def __iter__(self):
        return iter(self.next, None)

00213 class _RecordConsumer(AbstractConsumer):
    def __init__(self):
        self.enzyme_record = EnzymeRecord()
    def identification(self, id_info):
        self.enzyme_record.ID = id_info.split()[1]
    def description(self,de_info):
    def alternate_name(self,an_info):
    def catalytic_activity(self, ca_info):
        self.enzyme_record.CA = ''.join([self.enzyme_record.CA, ca_info[2:].strip()])
    def cofactor(self, cf_info):
    def comment(self, cc_info):
        cc = cc_info[2:].strip()
        if cc.startswith("-!-"):
            # The header is all CC, but doesn't start with -!-
            if self.enzyme_record.CC:
                pre_cc = self.enzyme_record.CC.pop()
                pre_cc = ""
            new_cc = pre_cc + " " + cc
    def disease(self, di_info):
    def prosite_reference(self,pr_info):

    def databank_reference(self,dr_info):
        good_data = dr_info[2:].strip()
        pair_data = good_data.split(';')
        for pair in pair_data:
            if not pair: continue
            data_record = DataRecord()
            t1, t2 = pair.split(',')
            data_record.tr_code, data_record.sw_code = \
                t1.strip(), t2.strip()

    def terminator(self,schwarzenegger):
        pass # Hasta la Vista, baby!

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