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__init__.py

# Copyright 2001 by Tarjei Mikkelsen.  All rights reserved.
# Copyright 2007 by Michiel de Hoon.  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.

"""
This module provides code to work with the KEGG Enzyme database.

Functions:
parse - Returns an iterator giving Record objects.

Classes:
Record               -- Holds the information from a KEGG Enzyme record.
"""

from Bio.KEGG import _write_kegg
from Bio.KEGG import _wrap_kegg


# Set up line wrapping rules (see Bio.KEGG._wrap_kegg)
rxn_wrap = [0, "",
            (" + ","",1,1),
            (" = ","",1,1),
            (" ","$",1,1),
            ("-","$",1,1)]
name_wrap = [0, "",
             (" ","$",1,1),
             ("-","$",1,1)]
id_wrap = lambda indent : [indent, "",
                           (" ","",1,0)]
struct_wrap = lambda indent : [indent, "",
                               ("  ","",1,1)]

00035 class Record:
    """Holds info from a KEGG Enzyme record.

    Members:
    entry       The EC number (withou the 'EC ').
    name        A list of the enzyme names.
    classname   A list of the classification terms.
    sysname     The systematic name of the enzyme.
    reaction    A list of the reaction description strings.
    substrate   A list of the substrates.
    product     A list of the products.
    inhibitor   A list of the inhibitors.
    cofactor    A list of the cofactors.
    effector    A list of the effectors.
    comment     A list of the comment strings.
    pathway     A list of 3-tuples: (database, id, pathway)
    genes       A list of 2-tuples: (organism, list of gene ids)
    disease     A list of 3-tuples: (database, id, disease)
    structures  A list of 2-tuples: (database, list of struct ids)
    dblinks     A list of 2-tuples: (database, list of db ids)
    """
00056     def __init__(self):
        """__init___(self)

        Create a new Record.
        """
        self.entry      = ""
        self.name       = []
        self.classname  = []
        self.sysname    = []
        self.reaction   = []
        self.substrate  = []
        self.product    = []
        self.inhibitor  = []
        self.cofactor   = []
        self.effector   = []
        self.comment    = []
        self.pathway    = []
        self.genes      = []
        self.disease    = []
        self.structures = []
        self.dblinks    = []
00077     def __str__(self):
        """__str__(self)

        Returns a string representation of this Record.
        """
        return self._entry() + \
               self._name()  + \
               self._classname() + \
               self._sysname() + \
               self._reaction() + \
               self._substrate() + \
               self._product() + \
               self._inhibitor() + \
               self._cofactor() + \
               self._effector() + \
               self._comment() + \
               self._pathway() + \
               self._genes() + \
               self._disease() + \
               self._structures() + \
               self._dblinks() + \
               "///"
    def _entry(self):
        return _write_kegg("ENTRY",
                           ["EC " + self.entry])
    def _name(self):
        return _write_kegg("NAME",
                           [_wrap_kegg(l, wrap_rule = name_wrap) \
                            for l in self.name])
    def _classname(self):
        return _write_kegg("CLASS",
                           self.classname)
    def _sysname(self):
        return _write_kegg("SYSNAME",
                           [_wrap_kegg(l, wrap_rule = name_wrap) \
                            for l in self.sysname])
    def _reaction(self):
        return _write_kegg("REACTION",
                           [_wrap_kegg(l, wrap_rule = rxn_wrap) \
                            for l in self.reaction])
    def _substrate(self):
        return _write_kegg("SUBSTRATE",
                           [_wrap_kegg(l, wrap_rule = name_wrap) \
                            for l in self.substrate])
    def _product(self):
        return _write_kegg("PRODUCT",
                           [_wrap_kegg(l, wrap_rule = name_wrap) \
                            for l in self.product])
    def _inhibitor(self):
        return _write_kegg("INHIBITOR",
                           [_wrap_kegg(l, wrap_rule = name_wrap) \
                            for l in self.inhibitor])
    def _cofactor(self):
        return _write_kegg("COFACTOR",
                           [_wrap_kegg(l, wrap_rule = name_wrap) \
                            for l in self.cofactor])
    def _effector(self):
        return _write_kegg("EFFECTOR",
                           [_wrap_kegg(l, wrap_rule = name_wrap) \
                            for l in self.effector])
    def _comment(self):
        return _write_kegg("COMMENT",
                           [_wrap_kegg(l, wrap_rule = id_wrap(0)) \
                            for l in self.comment])
    def _pathway(self):
        s = []
        for entry in self.pathway:
            s.append(entry[0] + ": " + entry[1] + "  " + entry[2])
        return _write_kegg("PATHWAY",
                           [_wrap_kegg(l, wrap_rule = id_wrap(16)) \
                            for l in s])
    def _genes(self):
        s = []
        for entry in self.genes:
            s.append(entry[0] + ": " + " ".join(entry[1]))
        return _write_kegg("GENES",
                           [_wrap_kegg(l, wrap_rule = id_wrap(5)) \
                            for l in s])
    def _disease(self):
        s = []
        for entry in self.disease:
            s.append(entry[0] + ": " + entry[1] + "  " + entry[2])
        return _write_kegg("DISEASE",
                           [_wrap_kegg(l, wrap_rule = id_wrap(13)) \
                            for l in s])    
    def _structures(self):
        s = []
        for entry in self.structures:
            s.append(entry[0] + ": " + "  ".join(entry[1]) + "  ")
        return _write_kegg("STRUCTURES",
                           [_wrap_kegg(l, wrap_rule = struct_wrap(5)) \
                            for l in s])
    def _dblinks(self):
        # This is a bit of a cheat that won't work if enzyme entries
        # have more than one link id per db id. For now, that's not
        # the case - storing links ids in a list is only to make
        # this class similar to the Compound.Record class.
        s = []
        for entry in self.dblinks:
            s.append(entry[0] + ": " + "  ".join(entry[1]))
        return _write_kegg("DBLINKS", s)



def parse(handle):
    """Parse a KEGG Enzyme file, returning Record objects.

    This is an iterator function, typically used in a for loop.  For
    example, using one of the example KEGG files in the Biopython
    test suite,

    >>> handle = open("KEGG/enzyme.sample")
    >>> for record in parse(handle):
    ...     print record.entry, record.name[0]
    ...
    1.1.1.1 Alcohol dehydrogenase
    1.1.1.62 Estradiol 17beta-dehydrogenase
    1.1.1.68 Transferred to EC 1.7.99.5
    1.6.5.3 NADH dehydrogenase (ubiquinone)
    1.14.13.28 3,9-Dihydroxypterocarpan 6a-monooxygenase
    2.4.1.68 Glycoprotein 6-alpha-L-fucosyltransferase
    3.1.1.6 Acetylesterase
    2.7.2.1 Acetate kinase
    """
    record = Record()
    for line in handle:
        if line[:3]=="///":
            yield record
            record = Record()
            continue
        if line[:12]!="            ":
            keyword = line[:12]
        data = line[12:].strip()
        if keyword=="ENTRY       ":
            words = data.split()
            record.entry = words[1]
        elif keyword=="CLASS       ":
            record.classname.append(data)
        elif keyword=="COFACTOR    ":
            record.cofactor.append(data)
        elif keyword=="COMMENT     ":
            record.comment.append(data)
        elif keyword=="DBLINKS     ":
            if ":" in data:
                key, values = data.split(":")
                values = values.split()
                row = (key, values)
                record.dblinks.append(row)
            else:
                row = record.dblinks[-1]
                key, values = row
                values.extend(data.split())
                row = key, values
                record.dblinks[-1] = row
        elif keyword=="DISEASE     ":
            if ":" in data:
                database, data = data.split(":")
                number, name = data.split(None, 1)
                row = (database, number, name)
                record.disease.append(row)
            else:
                row = record.disease[-1]
                database, number, name = row
                name = name + " " + data
                row = database, number, name
                record.disease[-1] = row
        elif keyword=="EFFECTOR    ":
             record.effector.append(data.strip(";"))
        elif keyword=="GENES       ":
            if data[3:5]==': ':
                key, values = data.split(":",1)
                values = [value.split("(")[0] for value in values.split()]
                row = (key, values)
                record.genes.append(row)
            else:
                row = record.genes[-1]
                key, values = row
                for value in data.split():
                    value = value.split("(")[0]
                    values.append(value)
                row = key, values
                record.genes[-1] = row
        elif keyword=="INHIBITOR   ":
             record.inhibitor.append(data.strip(";"))
        elif keyword=="NAME        ":
             record.name.append(data.strip(";"))
        elif keyword=="PATHWAY     ":
            if data[:5]=='PATH:':
                path, map, name = data.split(None,2)
                pathway = (path[:-1], map, name)
                record.pathway.append(pathway)
            else:
                pathway = record.pathway[-1]
                path, map, name = pathway
                name = name + " " + data
                pathway = path, map, name
                record.pathway[-1] = pathway
        elif keyword=="PRODUCT     ":
             record.product.append(data.strip(";"))
        elif keyword=="REACTION    ":
             record.reaction.append(data.strip(";"))
        elif keyword=="STRUCTURES  ":
            if data[:4]=='PDB:':
                database = data[:3]
                accessions = data[4:].split()
                row = (database, accessions)
                record.structures.append(row)
            else:
                row = record.structures[-1]
                database, accessions = row
                accessions.extend(data.split())
                row = (database, accessions)
                record.structures[-1] = row
        elif keyword=="SUBSTRATE   ":
             record.substrate.append(data.strip(";"))
        elif keyword=="SYSNAME     ":
             record.sysname.append(data.strip(";"))

def _test():
    """Run the Bio.KEGG.Enzyme module's doctests.
    
    This will try and locate the unit tests directory, and run the doctests
    from there in order that the relative paths used in the examples work.
    """
    import doctest
    import os
    if os.path.isdir(os.path.join("..","..","..","Tests")):
        print "Runing doctests..."
        cur_dir = os.path.abspath(os.curdir)
        os.chdir(os.path.join("..","..","..","Tests"))
        doctest.testmod()
        os.chdir(cur_dir)
        del cur_dir
        print "Done"

if __name__ == "__main__":
    _test()

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