Python String Examples

Example #1

File: pfamseq.py Project: ecolell/pfamserver

class Pfamseq(Base):
    pfamseq_acc = db.Column(
        db.String(10),
        primary_key=True)
    pfamseq_id = db.Column(
        db.String(16),
        index=True)

Example #2

File: pfam_a_pfamseq.py Project: ecolell/pfamserver

class PfamAPfamseq(db.Model):
    __tablename__ = 'pfamA_pfamseq'

    pfamseq_id = db.Column(db.String(40), index=True)
    pfamA_acc = db.Column(db.String(7), index=True)
    pfamseq_acc = db.Column(db.String(10), index=True)
    has_pdb = db.Column(db.Boolean, default=False)

    __table_args__ = (
        PrimaryKeyConstraint('pfamseq_id', 'pfamA_acc', 'pfamseq_acc'),
        {},
    )

Example #3

File: uniprot_reg_full.py Project: ecolell/pfamserver

class UniprotRegFull(db.Model):
    auto_uniprot_reg_full = db.Column(INTEGER(unsigned=True), primary_key=True)
    pfamA_acc = db.Column(db.String(7), db.ForeignKey('pfamA.pfamA_acc'))
    pfamA = db.relationship('PfamA', backref=db.backref('uniprots'))
    uniprot_acc = db.Column(db.String(10),
                            db.ForeignKey('uniprot.uniprot_acc'))
    uniprot = db.relationship('Uniprot', backref=db.backref('pfams'))
    seq_start = db.Column(db.Integer, index=True)
    seq_end = db.Column(db.Integer)
    in_full = db.Column(db.Integer, index=True)

    __table_args__ = (
        PrimaryKeyConstraint('pfamA_acc', 'uniprot_acc', 'seq_start',
                             'in_full'),
        {},
    )

Example #4

class Pdb(db.Model):
    pdb_id = db.Column(db.String(5), primary_key=True)
    title = db.Column(db.UnicodeText)
    method = db.Column(db.UnicodeText)
    resolution = db.Column(db.Numeric)
    author = db.Column(db.UnicodeText)
    date = db.Column(db.UnicodeText)

Example #5

File: pfam_a_reg_full_significant.py Project: ecolell/pfamserver

class PfamARegFullSignificant(db.Model):
    __tablename__ = 'pfamA_reg_full_significant'

    pfamA_acc = db.Column(
        db.String(7),
        index=True)
    pfamseq_acc = db.Column(
        db.String(10),
        index=True)
    seq_start = db.Column(
        db.Integer,
        index=True)
    seq_end = db.Column(
        db.Integer)
    in_full = db.Column(
        db.Integer,
        index=True)

    __table_args__ = (
        PrimaryKeyConstraint('pfamA_acc', 'pfamseq_acc', 'seq_start', 'in_full'),
        {},
    )

Example #6

File: pdb_pfam_a_reg.py Project: ecolell/pfamserver

class PdbPfamAReg(db.Model):
    __tablename__ = 'pdb_pfamA_reg'

    # auto_pfamA_reg_full = db.Column(
    #    db.Integer,
    #    primary_key=True)
    auto_uniprot_reg_full = db.Column(
        INTEGER(unsigned=True),
        db.ForeignKey('uniprot_reg_full.auto_uniprot_reg_full'))
    uniprot_reg_full = db.relationship('UniprotRegFull',
                                       backref=db.backref('pdbs'))
    pdb_id = db.Column(db.String(5), db.ForeignKey('pdb.pdb_id'))
    pdb = db.relationship('Pdb', backref=db.backref('pfams'))
    chain = db.Column(db.String(4), index=True)
    pfamA_acc = db.Column(db.String(7), index=True)
    pfamseq_acc = db.Column(db.String(10), index=True)
    pdb_res_start = db.Column(db.Integer, index=True)
    pdb_res_end = db.Column(db.Integer, index=True)

    __table_args__ = (
        PrimaryKeyConstraint('auto_uniprot_reg_full', 'pdb_id'),
        {},
    )

Example #7

class PfamA(Base):
    pfamA_acc = db.Column(db.String(7), primary_key=True)
    pfamA_id = db.Column(db.String(16), index=True, unique=True)
    description = db.Column(db.UnicodeText)
    num_full = db.Column(db.Integer)

Example #8

class Uniprot(Base):
    uniprot_acc = db.Column(db.String(10), primary_key=True)
    uniprot_id = db.Column(db.String(16), index=True, unique=True)
    description = db.Column(db.UnicodeText)