def lineage_id(self, acc_number_list):
"""Get taxonomic lineage name for accession ids
Given a list of accession numbers, yield the accession number and their
associated lineage (in the form of taxids) as tuples
Args:
acc_number_list (:obj:`list`): a list of accession numbers
Yields:
tuple: (accession id, lineage list)
"""
self.check_list_ids(acc_number_list)
with self.db.atomic():
query = Accession.select().where(
Accession.accession << acc_number_list)
for i in query:
lineage_list = []
current_lineage = i.taxid.tax_name
current_lineage_id = i.taxid.ncbi_taxid
parent = i.taxid.parent_taxid
while current_lineage != 'root':
lineage_list.append(current_lineage_id)
new_query = Taxa.get(Taxa.ncbi_taxid == parent)
current_lineage = new_query.tax_name
current_lineage_id = new_query.ncbi_taxid
parent = new_query.parent_taxid
yield (i.accession, lineage_list)
def lineage_id(self, acc_number_list):
"""Get taxonomic lineage name for accession ids
Given a list of accession numbers, yield the accession number and their
associated lineage (in the form of taxids) as tuples
Args:
acc_number_list (:obj:`list`): a list of accession numbers
Yields:
tuple: (accession id, lineage list)
"""
self.check_list_ids(acc_number_list)
with self.db.atomic():
query = Accession.select().where(
Accession.accession << acc_number_list)
for i in query:
lineage_list = []
current_lineage = i.taxid.tax_name
current_lineage_id = i.taxid.ncbi_taxid
parent = i.taxid.parent_taxid
while current_lineage != 'root':
lineage_list.append(current_lineage_id)
new_query = Taxa.get(Taxa.ncbi_taxid == parent)
current_lineage = new_query.tax_name
current_lineage_id = new_query.ncbi_taxid
parent = new_query.parent_taxid
yield (i.accession, lineage_list)
def sci_name(self, acc_number_list):
"""Get taxonomic scientific name for accession ids
Given a list of accession numbers, yield the accession number and their
associated scientific name as tuples
Args:
acc_number_list (:obj:`list`): a list of accession numbers
Yields:
tuple: (accession id, taxonomy id)
"""
self.check_list_ids(acc_number_list)
with self.db.atomic():
query = Accession.select().where(
Accession.accession << acc_number_list)
for i in query:
yield (i.accession, i.taxid.tax_name)
def sci_name(self, acc_number_list):
"""Get taxonomic scientific name for accession ids
Given a list of accession numbers, yield the accession number and their
associated scientific name as tuples
Args:
acc_number_list (:obj:`list`): a list of accession numbers
Yields:
tuple: (accession id, taxonomy id)
"""
self.check_list_ids(acc_number_list)
with self.db.atomic():
query = Accession.select().where(
Accession.accession << acc_number_list)
for i in query:
yield (i.accession, i.taxid.tax_name)