def to_jaspar(self, filename):
"""Writes the PWM to the given file in JASPAR format."""
jaspar_motif = jaspar.Motif(matrix_id=self.TF.accession_number,
name=self.name,
instances=self._motif.instances)
with open(filename, 'w') as f:
f.write(jaspar.write([jaspar_motif], 'jaspar'))
def _PSSM_model_to_jaspar(self, filename):
"""Writes the PSSM to the given file in jaspar format."""
header = self.strain_name
jaspar_motif = jaspar.Motif(matrix_id='',
name=header,
counts=self.TF_binding_model.pwm)
with open(filename, 'w') as f:
f.write(jaspar.write([jaspar_motif], 'jaspar'))
def _fetch_motif_by_internal_id(self, int_id):
"""Fetch basic motif information (PRIVATE)."""
cur = self.dbh.cursor()
cur.execute(
"select BASE_ID, VERSION, COLLECTION, NAME from MATRIX where id = %s",
(int_id,),
)
row = cur.fetchone()
# This should never happen as it is an internal method. If it does
# we should probably raise an exception
if not row:
warnings.warn(
f"Could not fetch JASPAR motif with internal ID = {int_id}",
BiopythonWarning,
)
return None
base_id = row[0]
version = row[1]
collection = row[2]
name = row[3]
matrix_id = "".join([base_id, ".", str(version)])
# fetch the counts matrix
counts = self._fetch_counts_matrix(int_id)
# Create new JASPAR motif
motif = jaspar.Motif(matrix_id, name, collection=collection, counts=counts)
# fetch species
cur.execute("select TAX_ID from MATRIX_SPECIES where id = %s", (int_id,))
tax_ids = []
rows = cur.fetchall()
for row in rows:
tax_ids.append(row[0])
# Many JASPAR motifs (especially those not in the CORE collection)
# do not have taxonomy IDs. So this warning would get annoying.
# if not tax_ids:
# warnings.warn("Could not fetch any taxonomy IDs for JASPAR motif"
# " {0}".format(motif.matrix_id), BiopythonWarning)
motif.species = tax_ids
# fetch protein accession numbers
cur.execute("select ACC FROM MATRIX_PROTEIN where id = %s", (int_id,))
accs = []
rows = cur.fetchall()
for row in rows:
accs.append(row[0])
# Similarly as for taxonomy IDs, it would get annoying to print
# warnings for JASPAR motifs which do not have accession numbers.
motif.acc = accs
# fetch remaining annotation as tags from the ANNOTATION table
cur.execute("select TAG, VAL from MATRIX_ANNOTATION where id = %s", (int_id,))
rows = cur.fetchall()
# Since JASPAR 2018 tf_family and tf_class are return as array.
tf_family = []
tf_class = []
for row in rows:
attr = row[0]
val = row[1]
if attr == "class":
tf_class.append(val)
elif attr == "family":
tf_family.append(val)
elif attr == "tax_group":
motif.tax_group = val
elif attr == "type":
motif.data_type = val
elif attr == "pazar_tf_id":
motif.pazar_id = val
elif attr == "medline":
motif.medline = val
elif attr == "comment":
motif.comment = val
else:
# TODO If we were to implement additional abitrary tags
# motif.tag(attr, val)
pass
motif.tf_family = tf_family
motif.tf_class = tf_class
return motif
def _fetch_motif_by_internal_id(self, int_id):
# fetch basic motif information
sql = "select BASE_ID, VERSION, COLLECTION, NAME from MATRIX where id = %d" % int_id
cur = self.dbh.cursor()
cur.execute(sql)
row = cur.fetchone()
base_id = row[0]
version = row[1]
collection = row[2]
name = row[3]
matrix_id = "".join([base_id, '.', str(version)])
# fetch the counts matrix
counts = self._fetch_counts_matrix(int_id)
# Create new JASPAR motif
motif = jaspar.Motif(
matrix_id, name, collection=collection, counts=counts
)
# fetch species
sql = "select TAX_ID from MATRIX_SPECIES where id = %d" % int_id
cur.execute(sql)
tax_ids = []
rows = cur.fetchall()
for row in rows:
tax_ids.append(row[0])
motif.species = tax_ids
# fetch protein accession numbers
sql = "select ACC FROM MATRIX_PROTEIN where id = %d" % int_id
cur.execute(sql)
accs = []
rows = cur.fetchall()
for row in rows:
accs.append(row[0])
motif.acc = accs
# fetch remaining annotation as tags from the ANNOTATION table
sql = "select TAG, VAL from MATRIX_ANNOTATION where id = %d" % int_id
cur.execute(sql)
rows = cur.fetchall()
for row in rows:
attr = row[0]
val = row[1]
if attr == 'class':
motif.tf_class = val
elif attr == 'family':
motif.tf_family = val
elif attr == 'tax_group':
motif.tax_group = val
elif attr == 'type':
motif.data_type = val
elif attr == 'pazar_tf_id':
motif.pazar_id = val
elif attr == 'medline':
motif.medline = val
elif attr == 'comment':
motif.comment = val
else:
"""
TODO If we were to implement additional abitrary tags
motif.tag(attr, val)
"""
pass
return motif
