class metadata_m(DictSerializable, db_2.Model):
"""
Table for storing information about other tables
"""
__tablename__ = "metadata"
key = db_2.Column(db_2.String(50), index=True, primary_key=True)
value = db_2.Column(db_2.String)
class homologs_m(DictSerializable, db_2.Model):
"""
The homologs database combines
"""
__tablename__ = "homologs"
id = db_2.Column(db_2.Integer, primary_key=True)
gene_id = db_2.Column(db_2.ForeignKey('wormbase_gene_summary.gene_id'),
nullable=False,
index=True)
gene_name = db_2.Column(db_2.String(40), index=True)
homolog_species = db_2.Column(db_2.String(50), index=True)
homolog_taxon_id = db_2.Column(db_2.Integer, index=True,
nullable=True) # If available
homolog_gene = db_2.Column(db_2.String(50), index=True)
homolog_source = db_2.Column(db_2.String(40))
gene_summary = db_2.relationship("wormbase_gene_summary_m",
backref='homologs',
lazy='joined')
def unnest(self):
"""
Used with the gene API - returns
an unnested homolog datastructure combined with the wormbase gene summary model.
"""
self.__dict__.update(self.gene_summary.__dict__)
self.__dict__['gene_summary'] = None
return self
def __repr__(self):
return f"homolog: {self.gene_name} -- {self.homolog_gene}"
class wormbase_gene_summary_m(DictSerializable, db_2.Model):
"""
This is a condensed version of the wormbase_gene_m model;
It is constructed out of convenience and only defines the genes
(not exons/introns/etc.)
"""
__tablename__ = "wormbase_gene_summary"
id = db_2.Column(db_2.Integer, primary_key=True)
chrom = db_2.Column(db_2.String(7), index=True)
chrom_num = db_2.Column(db_2.Integer(), index=True)
start = db_2.Column(db_2.Integer(), index=True)
end = db_2.Column(db_2.Integer(), index=True)
locus = db_2.Column(db_2.String(30), index=True)
gene_id = db_2.Column(db_2.String(25), index=True)
gene_id_type = db_2.Column(db_2.String(15), index=False)
sequence_name = db_2.Column(db_2.String(30), index=True)
biotype = db_2.Column(db_2.String(30), nullable=True)
gene_symbol = db_2.column_property(
func.coalesce(locus, sequence_name, gene_id))
interval = db_2.column_property(func.printf("%s:%s-%s", chrom, start, end))
arm_or_center = db_2.Column(db_2.String(12), index=True)
@classmethod
def resolve_gene_id(cls, query):
"""
query - a locus name or transcript ID
output - a wormbase gene ID
Example:
wormbase_gene_m.resolve_gene_id('pot-2') --> WBGene00010195
"""
result = cls.query.filter(
or_(cls.locus == query, cls.sequence_name == query)).first()
if result:
return result.gene_id
class wormbase_gene_m(DictSerializable, db_2.Model):
__tablename__ = 'wormbase_gene'
id = db_2.Column(db_2.Integer, primary_key=True)
chrom = db_2.Column(db_2.String(20), index=True)
chrom_num = db_2.Column(db_2.Integer(), index=True) # For sorting purposes
start = db_2.Column(db_2.Integer(), index=True)
end = db_2.Column(db_2.Integer(), index=True)
feature = db_2.Column(db_2.String(30), index=True)
strand = db_2.Column(db_2.String(1))
frame = db_2.Column(db_2.Integer(), nullable=True)
gene_id = db_2.Column(db_2.ForeignKey('wormbase_gene_summary.gene_id'),
nullable=False)
gene_biotype = db_2.Column(db_2.String(30), nullable=True)
locus = db_2.Column(db_2.String(30), index=True)
transcript_id = db_2.Column(db_2.String(30), nullable=True, index=True)
transcript_biotype = db_2.Column(db_2.String(), index=True)
exon_id = db_2.Column(db_2.String(30), nullable=True, index=True)
exon_number = db_2.Column(db_2.Integer(), nullable=True)
protein_id = db_2.Column(db_2.String(30), nullable=True, index=True)
arm_or_center = db_2.Column(db_2.String(12), index=True)
gene_summary = db_2.relationship("wormbase_gene_summary_m",
backref='gene_components')
def __repr__(self):
return f"{self.gene_id}:{self.feature} [{self.seqname}:{self.start}-{self.end}]"
class strain_m(DictSerializable, db_2.Model):
__tablename__ = "strain"
strain = db_2.Column(db_2.String(25), primary_key=True)
reference_strain = db_2.Column(db_2.Boolean(), index=True)
sequenced = db_2.Column(db_2.Boolean(), index=True, nullable=True)
isotype = db_2.Column(db_2.String(25), index=True, nullable=True)
previous_names = db_2.Column(db_2.String(100), nullable=True)
source_lab = db_2.Column(db_2.String(), nullable=True)
release = db_2.Column(db_2.Integer(), nullable=False, index=True)
latitude = db_2.Column(db_2.Float(), nullable=True)
longitude = db_2.Column(db_2.Float(), nullable=True)
elevation = db_2.Column(db_2.Float(), nullable=True)
landscape = db_2.Column(db_2.String(), nullable=True)
substrate = db_2.Column(db_2.String(), nullable=True)
photo = db_2.Column(db_2.String(), nullable=True)
isolated_by = db_2.Column(db_2.String(), nullable=True)
sampled_by = db_2.Column(db_2.String(), nullable=True)
isolation_date = db_2.Column(db_2.Date(), nullable=True)
isolation_date_comment = db_2.Column(db_2.String(), nullable=True)
notes = db_2.Column(db_2.String(), nullable=True)
sets = db_2.Column(db_2.String(), nullable=True)
c_label = db_2.Column(db_2.String(), nullable=True)
s_label = db_2.Column(db_2.String(), nullable=True)
substrate_temp = db_2.Column(db_2.Float())
ambient_temp = db_2.Column(db_2.Float())
substrate_moisture = db_2.Column(db_2.Float())
ambient_humidity = db_2.Column(db_2.Float())
def __repr__(self):
return self.strain
def to_json(self):
return {
k: v
for k, v in self.__dict__.items() if not k.startswith("_")
}
def list_sets(self):
if self.sets:
return self.sets.split(",")
else:
return []
def bam_url(self):
"""
Return bam / bam_index url set
"""
url_set = Markup(f"""
<a href="{URLS.BAM_URL_PREFIX}/{self.isotype}.bam">
BAM
</a>
/
<a href="{URLS.BAM_URL_PREFIX}/{self.isotype}.bam.bai">
bai
</a>
""".strip())
return url_set
@classmethod
def cum_sum_strain_isotype(cls):
"""
Create a time-series plot of strains and isotypes collected over time
Args:
df - the strain dataset
"""
df = pd.read_sql_table(cls.__tablename__, db_2.engine)
cumulative_isotype = df[['isotype', 'isolation_date']].sort_values(['isolation_date'], axis=0) \
.drop_duplicates(['isotype']) \
.groupby(['isolation_date'], as_index=True) \
.count() \
.cumsum() \
.reset_index()
cumulative_isotype = cumulative_isotype.append(
{
'isolation_date':
np.datetime64(datetime.datetime.today().strftime("%Y-%m-%d")),
'isotype':
len(df['isotype'].unique())
},
ignore_index=True)
cumulative_strain = df[['strain', 'isolation_date']].sort_values(['isolation_date'], axis=0) \
.drop_duplicates(['strain']) \
.dropna(how='any') \
.groupby(['isolation_date']) \
.count() \
.cumsum() \
.reset_index()
cumulative_strain = cumulative_strain.append(
{
'isolation_date':
np.datetime64(datetime.datetime.today().strftime("%Y-%m-%d")),
'strain':
len(df['strain'].unique())
},
ignore_index=True)
df = cumulative_isotype.set_index('isolation_date') \
.join(cumulative_strain.set_index('isolation_date')) \
.reset_index()
return df
@classmethod
def release_summary(cls, release):
"""
Returns isotype and strain count for a data release.
Args:
release - the data release
"""
counts = {
'strain_count':
cls.query.filter((cls.release <= release)).count(),
'strain_count_sequenced':
cls.query.filter((cls.release <= release)
& (cls.sequenced == True)).count(),
'isotype_count':
cls.query.filter(cls.release <= release).group_by(
cls.isotype).count()
}
return counts
def as_dict(self):
return {c.name: getattr(self, c.name) for c in self.__table__.columns}
