def get_exon (cursor, exon_id, is_known=None, db_name=None):
exon = Exon ()
if (db_name):
if not switch_to_db(cursor, db_name):
return exon
if is_known==2:
# sw# exon
qry = "select * from sw_exon where exon_id = %d" % exon_id
rows = search_db(cursor, qry, verbose=False)
if (not rows):
return exon
exon.load_from_novel_exon (rows[0], "sw_exon")
elif is_known==3:
# sw# exon
qry = "select * from usearch_exon where exon_id = %d" % exon_id
rows = search_db(cursor, qry, verbose=False)
if (not rows):
return exon
exon.load_from_novel_exon (rows[0], "usearch_exon")
else:
qry = "select * from gene2exon where exon_id = %d" % exon_id
if is_known: qry += " and is_known = %s " % is_known
rows = search_db(cursor, qry, verbose=False)
if (not rows):
return exon
exon.load_from_gene2exon (rows[0])
return exon
def taxid2parentid (cursor, tax_id):
qry = "select parent_tax_id from nodes where tax_id= %d " % tax_id
rows = search_db (cursor, qry)
if (not rows):
rows = search_db (cursor, qry, verbose = True)
return ""
return rows[0][0]
def get_species (cursor):
ensembl_db_name = {}
all_species = []
# find the release number
qry = "select value from exolocator_config.parameter where name = 'ensembl_release_number'"
rows = search_db(cursor, qry)
if not rows or 'error' in rows[0][0].lower():
print 'ensembl_release_number not set in exolocator_config'
exit(1)
release_number = rows[0][0]
qry = "show databases like '%core_{0}%'".format(release_number)
rows = search_db(cursor, qry)
if (not rows):
print "No databases with 'core_{0}' in the name found".format(release_number)
exit(1)
for row in rows:
db_name = row[0]
name_token = db_name.split ('_')
species = name_token[0]
i = 1
while not name_token[i] == 'core':
species += "_"+ name_token[i]
i += 1
ensembl_db_name[species] = db_name
all_species.append(species)
return all_species, ensembl_db_name
def get_alt_seq_info (cursor, gene_id, species):
# seq identifier from gene table
qry = "select seq_region_id, seq_region_start, seq_region_end, seq_region_strand from gene where gene_id = %d" % gene_id
rows = search_db (cursor, qry)
if not rows: return []
[seq_region_id, orig_seq_region_start, orig_seq_region_end, seq_region_strand] = rows[0]
# check whether we have "assembly exception"
# we do not want 'PAR' regions, though:
'''
The pseudo-autosomal regions are homologous DNA sequences on the (human) X and Y chromosomes.
They allow the pairing and crossing-over of these sex chromosomes the same way the autosomal
chromosomes do during meiosis.
As these genomic regions are identical between X and Y, they are oftentimes only stored once.
The exception types we are interested in are PATCH_FIX and PATCH_NOVEL
'''
qry = "select seq_region_start, seq_region_end, exc_seq_region_id, exc_seq_region_start, exc_seq_region_end "
qry += "from assembly_exception where seq_region_id = %d " % seq_region_id
qry += "and assembly_exception.exc_type like 'PATCH_%'"
rows = search_db (cursor, qry)
if not rows: return []
[seq_region_start, seq_region_end, exc_seq_region_id, exc_seq_region_start, exc_seq_region_end] = rows[0]
qry = "select name, file_name from seq_region where seq_region_id= %d" % exc_seq_region_id
rows = search_db (cursor, qry)
if not rows: return []
[seq_name, file_names] = rows[0]
mitochondrial = is_mitochondrial (cursor, gene_id)
return [seq_name, file_names, seq_region_start, seq_region_end, seq_region_strand, mitochondrial]
def get_exon_pepseq(cursor, exon, db_name=None, verbose=False):
if db_name:
if not switch_to_db(cursor, db_name):
return False
if exon.exon_seq_id:
exon_seq_id = exon.exon_seq_id
qry = "select protein_seq "
qry += " from exon_seq where exon_seq_id = %d" % exon_seq_id
else:
exon_id = exon.exon_id
is_known = exon.is_known
qry = "select protein_seq "
qry += " from exon_seq where exon_id = %d and is_known = %d" % (exon_id, is_known)
rows = search_db(cursor, qry)
if not rows:
if verbose:
rows = search_db(cursor, qry, verbose=True)
print rows
return ""
protein_seq = rows[0][0]
if protein_seq is None:
protein_seq = ""
return protein_seq
def get_exon_pepseq (cursor, exon, db_name=None, verbose=False):
if (db_name):
if not switch_to_db(cursor, db_name):
return False
if exon.exon_seq_id:
exon_seq_id = exon.exon_seq_id
qry = "select protein_seq "
qry += " from exon_seq where exon_seq_id = %d" % exon_seq_id
else:
exon_id = exon.exon_id
is_known = exon.is_known
qry = "select protein_seq "
qry += " from exon_seq where exon_id = %d and is_known = %d" % (exon_id, is_known)
rows = search_db(cursor, qry)
if (not rows):
if verbose:
rows = search_db(cursor, qry, verbose = True)
print rows
return ""
protein_seq = rows[0][0]
if (protein_seq is None):
protein_seq = ""
return protein_seq
def is_reference(cursor, gene_id, non_ref_id, db_name=None):
if db_name:
qry = "use %s " % db_name
rows = search_db(cursor, qry)
if rows:
rows = search_db(cursor, qry, verbose=True)
print rows
exit(1)
qry = "select seq_region_id from gene where gene_id=%d" % int(gene_id)
rows = search_db(cursor, qry)
if not rows:
return True
seq_region_id = rows[0]
qry = "select attrib_type_id from seq_region_attrib where seq_region_id=%s" % seq_region_id
rows = search_db(cursor, qry)
if not rows:
return True
for row in rows:
attrib_type_id = int(row[0])
if attrib_type_id == non_ref_id:
return False
return True
def get_species(cursor):
ensembl_db_name = {}
all_species = []
# find the release number
qry = "select value from exolocator_config.parameter where name = 'ensembl_release_number'"
rows = search_db(cursor, qry)
if not rows or "error" in rows[0][0].lower():
print "ensembl_release_number not set in exolocator_config"
exit(1)
release_number = rows[0][0]
qry = "show databases like '%core_{0}%'".format(release_number)
rows = search_db(cursor, qry)
if not rows:
print "No databases with 'core_{0}' in the name found".format(release_number)
exit(1)
for row in rows:
db_name = row[0]
name_token = db_name.split("_")
species = name_token[0]
i = 1
while not name_token[i] == "core":
species += "_" + name_token[i]
i += 1
ensembl_db_name[species] = db_name
all_species.append(species)
return all_species, ensembl_db_name
def gene2exon_list(cursor, gene_id, db_name=None, verbose=False):
exons = []
if db_name:
if not switch_to_db(cursor, db_name):
return False
qry = "select * from gene2exon where gene_id = %d " % gene_id
rows = search_db(cursor, qry)
if not rows:
rows = search_db(cursor, "select database()")
if verbose:
print "database ", rows[0][0]
rows = search_db(cursor, qry, verbose=True)
print rows
return []
for row in rows:
exon = Exon()
if not exon.load_from_gene2exon(row):
continue
exons.append(exon)
return exons
def get_exon(cursor, exon_id, is_known=None, db_name=None):
exon = Exon()
if db_name:
if not switch_to_db(cursor, db_name):
return exon
if is_known == 2:
# sw# exon
qry = "select * from sw_exon where exon_id = %d" % exon_id
rows = search_db(cursor, qry, verbose=False)
if not rows:
return exon
exon.load_from_novel_exon(rows[0], "sw_exon")
elif is_known == 3:
# sw# exon
qry = "select * from usearch_exon where exon_id = %d" % exon_id
rows = search_db(cursor, qry, verbose=False)
if not rows:
return exon
exon.load_from_novel_exon(rows[0], "usearch_exon")
else:
qry = "select * from gene2exon where exon_id = %d" % exon_id
if is_known:
qry += " and is_known = %s " % is_known
rows = search_db(cursor, qry, verbose=False)
if not rows:
return exon
exon.load_from_gene2exon(rows[0])
return exon
def get_ncbi_tax_name(cursor):
qry = "show databases like 'ncbi%tax%'"
rows = search_db(cursor, qry)
if (not rows):
rows = search_db(cursor, qry, verbose=True)
return ""
return rows[0][0]
def get_ncbi_tax_name (cursor):
qry = "show databases like 'ncbi%tax%'"
rows = search_db (cursor, qry)
if (not rows):
rows = search_db (cursor, qry, verbose = True)
return ""
return rows[0][0]
def gene2exon_list (cursor, gene_id, db_name=None, verbose=False):
exons = []
if (db_name):
if not switch_to_db(cursor, db_name):
return False
qry = "select * from gene2exon where gene_id = %d " % gene_id
rows = search_db(cursor, qry)
if (not rows):
rows = search_db(cursor, 'select database()')
if verbose:
print "database ", rows[0][0]
rows = search_db(cursor, qry, verbose = True)
print rows
return []
for row in rows:
exon = Exon()
if (not exon.load_from_gene2exon(row)):
continue
exons.append(exon)
return exons
def get_canonical_coordinates(cursor, canonical_transcript_id):
qry = "select seq_start, start_exon_id, seq_end, end_exon_id "
qry += " from translation where transcript_id = %d " % canonical_transcript_id
rows = search_db(cursor, qry)
if not rows:
search_db(cursor, qry, verbose=True)
return []
return rows[0]
def get_canonical_coordinates (cursor, canonical_transcript_id):
qry = "select seq_start, start_exon_id, seq_end, end_exon_id "
qry += " from translation where transcript_id = %d " % canonical_transcript_id
rows = search_db (cursor, qry)
if ( not rows):
search_db (cursor, qry, verbose = True)
return []
return rows[0]
def get_orthologues_from_species(cursor, ensembl_db_name, ortho_type, gene_member_id, species):
# the ortho_type is one of the following: 'ortholog_one2one',
# 'ortholog_one2many', 'ortholog_many2many', 'possible_ortholog', 'apparent_ortholog_one2one'
orthos = []
# find genome db_id
genome_db_id = species2genome_db_id (cursor, species)
# make the cursor point to compara database - should be the responsibility of each function
switch_to_db (cursor, get_compara_name (cursor))
qry = "select homology.homology_id from homology_member, homology "
qry += " where homology_member.gene_member_id =%d " % gene_member_id
qry += " and homology.homology_id = homology_member.homology_id "
qry += " and homology.description = '%s' " % ortho_type
rows = search_db (cursor, qry)
if (not rows):
return [] # no orthologs here
# for each homology id find the other member id
#print qry
#print member_id, ortho_type, species, genome_db_id
#print rows
for row in rows:
homology_id = row[0]
#print "\t homology id:", homology_id
switch_to_db (cursor, get_compara_name (cursor))
qry = "select gene_member_id from homology_member "
qry += " where homology_id = %d" % int(homology_id)
qry += " and not gene_member_id = %d" % gene_member_id
rows2 = search_db (cursor, qry, verbose = False)
if (not rows2):
#print "\t ",
#rows2 = search_db (cursor, qry, verbose = True)
continue
for row2 in rows2:
ortho_id = row2[0]
#print "\t\t ortho id:", ortho_id
qry = "select stable_id from gene_member "
qry += " where gene_member_id = %d " % ortho_id
qry += " and genome_db_id = %d " % genome_db_id
rows3 = search_db (cursor, qry, verbose = False)
if (not rows3):
#print "\t\t ",
#rows3 = search_db (cursor, qry, verbose = True)
continue
ortho_stable = rows3[0][0]
#print "\t\t ortho stable:", ortho_stable
orthos.append(ortho_stable)
if orthos:
switch_to_db (cursor, ensembl_db_name [species])
orthos = map (lambda gene_id: stable2gene(cursor, gene_id), orthos)
#print 'orthos:', orthos
return orthos
def taxid2name(cursor, tax_id):
switch_to_db(cursor, get_ncbi_tax_name(cursor))
qry = "select name_txt from names where tax_id= %d " % int(tax_id)
qry += " and name_class = 'scientific name'"
rows = search_db(cursor, qry)
if (not rows):
rows = search_db(cursor, qry, verbose=True)
return ""
return rows[0][0]
def taxid2trivial(cursor, tax_id):
switch_to_db(cursor, get_ncbi_tax_name(cursor))
qry = "select name_txt from names where tax_id= %d " % int(tax_id)
qry += " and name_class = 'trivial'"
rows = search_db(cursor, qry)
if (not rows or 'ERROR' in rows[0]):
rows = search_db(cursor, qry, verbose=True)
return ""
return rows[0][0]
def get_orthologues_from_species(cursor, ensembl_db_name, ortho_type, gene_member_id, species):
# the ortho_type is one of the following: 'ortholog_one2one',
# 'ortholog_one2many', 'ortholog_many2many', 'possible_ortholog', 'apparent_ortholog_one2one'
orthos = []
# find genome db_id
genome_db_id = species2genome_db_id(cursor, species)
# make the cursor point to compara database - should be the responsibility of each function
switch_to_db(cursor, get_compara_name(cursor))
qry = "select homology.homology_id from homology_member, homology "
qry += " where homology_member.gene_member_id =%d " % gene_member_id
qry += " and homology.homology_id = homology_member.homology_id "
qry += " and homology.description = '%s' " % ortho_type
rows = search_db(cursor, qry)
if not rows:
return [] # no orthologs here
# for each homology id find the other member id
# print qry
# print member_id, ortho_type, species, genome_db_id
# print rows
for row in rows:
homology_id = row[0]
# print "\t homology id:", homology_id
switch_to_db(cursor, get_compara_name(cursor))
qry = "select gene_member_id from homology_member "
qry += " where homology_id = %d" % int(homology_id)
qry += " and not gene_member_id = %d" % gene_member_id
rows2 = search_db(cursor, qry, verbose=False)
if not rows2:
# print "\t ",
# rows2 = search_db (cursor, qry, verbose = True)
continue
for row2 in rows2:
ortho_id = row2[0]
# print "\t\t ortho id:", ortho_id
qry = "select stable_id from gene_member "
qry += " where gene_member_id = %d " % ortho_id
qry += " and genome_db_id = %d " % genome_db_id
rows3 = search_db(cursor, qry, verbose=False)
if not rows3:
# print "\t\t ",
# rows3 = search_db (cursor, qry, verbose = True)
continue
ortho_stable = rows3[0][0]
# print "\t\t ortho stable:", ortho_stable
orthos.append(ortho_stable)
if orthos:
switch_to_db(cursor, ensembl_db_name[species])
orthos = map(lambda gene_id: stable2gene(cursor, gene_id), orthos)
# print 'orthos:', orthos
return orthos
def trivial2taxid (cursor, trivial_name):
switch_to_db (cursor, get_ncbi_tax_name (cursor))
qry = "select tax_id from names where name_txt= '%s' " % trivial_name
qry += " and name_class = 'trivial'";
rows = search_db (cursor, qry)
if (not rows or 'ERROR' in rows[0]):
rows = search_db (cursor, qry, verbose = True)
return ""
return int(rows[0][0])
def trivial2taxid(cursor, trivial_name):
switch_to_db(cursor, get_ncbi_tax_name(cursor))
qry = "select tax_id from names where name_txt= '%s' " % trivial_name
qry += " and name_class = 'trivial'"
rows = search_db(cursor, qry)
if (not rows or 'ERROR' in rows[0]):
rows = search_db(cursor, qry, verbose=True)
return ""
return int(rows[0][0])
def taxid2trivial (cursor, tax_id):
switch_to_db (cursor, get_ncbi_tax_name (cursor))
qry = "select name_txt from names where tax_id= %d " % int(tax_id)
qry += " and name_class = 'trivial'";
rows = search_db (cursor, qry)
if (not rows or 'ERROR' in rows[0]):
rows = search_db (cursor, qry, verbose = True)
return ""
return rows[0][0]
def taxid2name (cursor, tax_id):
switch_to_db (cursor, get_ncbi_tax_name (cursor))
qry = "select name_txt from names where tax_id= %d " % int(tax_id)
qry += " and name_class = 'scientific name'";
rows = search_db (cursor, qry)
if (not rows):
rows = search_db (cursor, qry, verbose = True)
return ""
return rows[0][0]
def get_gene_ids(cursor, db_name=None, biotype=None, is_known=None, ref_only=False):
gene_ids = []
if db_name:
qry = "use %s " % db_name
rows = search_db(cursor, qry)
if rows:
rows = search_db(cursor, qry, verbose=True)
print rows
exit(1)
qry = "select gene_id from gene"
if biotype or not is_known is None:
qry += " where "
if biotype:
qry += "biotype='%s'" % biotype
if biotype and not is_known is None:
qry += " and "
if not is_known is None:
if is_known:
qry += "status='known'"
else:
qry += "status!='known'"
rows = search_db(cursor, qry, verbose=False)
if not rows:
rows = search_db(cursor, qry, verbose=True)
return []
else:
if "Error" in rows[0]:
print rows[0]
return []
# I don't want to hard code the id for the annotation "non_ref"
# and I do no know where else to do it, so qe do it here
if ref_only:
qry = "select attrib_type_id from attrib_type where code='non_ref'"
rows2 = search_db(cursor, qry)
if not rows2 or not type(rows2[0][0]) is int:
ref_only = False
else:
non_ref_id = int(rows2[0][0])
for row in rows:
if not type(row[0]) is long:
print row
exit(1)
gene_id = int(row[0])
if ref_only and not is_reference(cursor, gene_id, non_ref_id):
continue
gene_ids.append(gene_id)
return gene_ids
def get_gene_ids (cursor, db_name=None, biotype = None, is_known = None, ref_only = False):
gene_ids = []
if (db_name):
qry = "use %s " % db_name
rows = search_db (cursor, qry)
if (rows):
rows = search_db (cursor, qry, verbose = True)
print rows
exit (1)
qry = "select gene_id from gene"
if ( biotype or not is_known is None):
qry += " where "
if ( biotype):
qry += "biotype='%s'" % biotype
if (biotype and not is_known is None):
qry += " and "
if (not is_known is None):
if is_known:
qry += "status='known'"
else:
qry += "status!='known'"
rows = search_db (cursor, qry, verbose = False)
if (not rows):
rows = search_db (cursor, qry, verbose = True)
return []
else:
if ('Error' in rows[0]):
print rows[0]
return []
# I don't want to hard code the id for the annotation "non_ref"
# and I do no know where else to do it, so qe do it here
if ref_only:
qry = "select attrib_type_id from attrib_type where code='non_ref'"
rows2 = search_db (cursor, qry)
if not rows2 or not type(rows2[0][0]) is int:
ref_only = False
else:
non_ref_id = int (rows2[0][0])
for row in rows:
if ( not type(row[0]) is long ):
print row
exit(1)
gene_id = int(row[0])
if ref_only and not is_reference(cursor, gene_id, non_ref_id): continue
gene_ids.append(gene_id)
return gene_ids
def get_species_shorthand(cursor, species):
db_name = get_compara_name (cursor)
qry = "use %s " % db_name
search_db (cursor, qry)
qry = "select shorthand from species_name_shorthands where species='%s'" % species
rows = search_db (cursor, qry)
if not rows: return ""
return rows[0][0]
def member2stable(cursor, member_id):
# member_id refers to compara db
# of which we need to have one
qry = "select stable_id from gene_member where gene_member_id = %d" % member_id
rows = search_db(cursor, qry)
if not rows:
rows = search_db(cursor, qry, verbose=True)
return ""
return rows[0][0]
def member2stable (cursor, member_id):
# member_id refers to compara db
# of which we need to have one
qry = "select stable_id from gene_member where gene_member_id = %d" % member_id
rows = search_db (cursor, qry)
if (not rows):
rows = search_db (cursor, qry, verbose = True)
return ""
return rows[0][0]
def species2genome_db_id(cursor, species):
switch_to_db(cursor, get_compara_name(cursor))
qry = "select genome_db_id from genome_db where name = '%s'" % species
rows = search_db(cursor, qry)
if not rows:
search_db(cursor, qry, verbose=True)
return 0
return int(rows[0][0])
def genome_db_id2species(cursor, genome_db_id):
switch_to_db(cursor, get_compara_name(cursor))
qry = "select name from genome_db where genome_db_id = %d" % int(genome_db_id)
rows = search_db(cursor, qry)
if not rows:
search_db(cursor, qry, verbose=True)
return ""
return rows[0][0]
def taxid2parentid (cursor, tax_id):
switch_to_db (cursor, get_ncbi_tax_name (cursor))
qry = "select parent_tax_id from nodes where tax_id= %d " % int(tax_id)
rows = search_db (cursor, qry)
if (not rows):
rows = search_db (cursor, qry, verbose = True)
return ""
try:
retval = int(rows[0][0])
except:
retval = ""
return retval
def taxid2parentid(cursor, tax_id):
switch_to_db(cursor, get_ncbi_tax_name(cursor))
qry = "select parent_tax_id from nodes where tax_id= %d " % int(tax_id)
rows = search_db(cursor, qry)
if (not rows):
rows = search_db(cursor, qry, verbose=True)
return ""
try:
retval = int(rows[0][0])
except:
retval = ""
return retval
def species2genome_db_id (cursor, species):
switch_to_db (cursor, get_compara_name (cursor))
qry = "select genome_db_id from genome_db where name = '%s'" % species
rows = search_db (cursor, qry)
if (not rows):
search_db (cursor, qry, verbose = True)
return 0
return int(rows[0][0])
def genome_db_id2species (cursor, genome_db_id):
switch_to_db (cursor, get_compara_name (cursor))
qry = "select name from genome_db where genome_db_id = %d" % int(genome_db_id)
rows = search_db (cursor, qry)
if (not rows):
search_db (cursor, qry, verbose = True)
return ""
return rows[0][0]
def stable2member (cursor, stable_id):
# member_id refers to compara db
# of which we need to have one
# qry = "select member_id from member where stable_id = '%s'" % stable_id
# since version 76 the table is called gene_member, and the main id is gene_member_id
qry = "select gene_member_id from gene_member where stable_id = '%s'" % stable_id
rows = search_db (cursor, qry)
if (not rows or 'ERROR' in rows[0]):
rows = search_db (cursor, qry, verbose = True)
exit(1)
return ""
return int(rows[0][0])
def species2taxid (cursor, species):
switch_to_db (cursor, get_compara_name (cursor))
qry = "select taxon_id from genome_db where name = '%s'" % species
rows = search_db (cursor, qry)
if (not rows):
search_db (cursor, qry, verbose = True)
return ""
try:
retval = int(rows[0][0])
except:
retval = ""
return retval
def species2taxid(cursor, species):
switch_to_db(cursor, get_compara_name(cursor))
qry = "select taxon_id from genome_db where name = '%s'" % species
rows = search_db(cursor, qry)
if not rows:
search_db(cursor, qry, verbose=True)
return ""
try:
retval = int(rows[0][0])
except:
retval = ""
return retval
def stable2member(cursor, stable_id):
# member_id refers to compara db
# of which we need to have one
# qry = "select member_id from member where stable_id = '%s'" % stable_id
# since version 76 the table is called gene_member, and the main id is gene_member_id
qry = "select gene_member_id from gene_member where stable_id = '%s'" % stable_id
rows = search_db(cursor, qry)
if not rows or "ERROR" in rows[0]:
rows = search_db(cursor, qry, verbose=True)
exit(1)
return ""
return int(rows[0][0])
def gene2canon_transl(cursor, gene_id, db_name=None,):
if (db_name and not switch_to_db(cursor, db_name)):
return False
qry = "select translation.translation_id from translation, gene "
qry += " where gene.canonical_transcript_id = translation.transcript_id "
qry += " and gene.gene_id = %d " % gene_id
rows = search_db (cursor, qry, verbose = False)
if (not rows):
rows = search_db (cursor, qry, verbose = True)
return ""
return rows[0][0]
def gene2stable_canon_transl(cursor, gene_id, db_name=None):
if db_name and not switch_to_db(cursor, db_name):
return False
qry = "select translation.stable_id from translation, gene "
qry += " where gene.canonical_transcript_id = translation.transcript_id "
qry += " and gene.gene_id = %d " % gene_id
rows = search_db(cursor, qry, verbose=False)
if not rows:
rows = search_db(cursor, qry, verbose=True)
return ""
return rows[0][0]
def get_exon_seq_by_db_id(cursor, exon_seq_id, db_name=None):
if db_name:
if not switch_to_db(cursor, db_name):
return False
qry = "select exon_seq_id, protein_seq, pepseq_transl_start, pepseq_transl_end, "
qry += " left_flank, right_flank, dna_seq "
qry += " from exon_seq where exon_seq_id = %d" % exon_seq_id
rows = search_db(cursor, qry)
if not rows:
# rows = search_db(cursor, qry, verbose = True)
return []
[exon_seq_id, protein_seq, pepseq_transl_start, pepseq_transl_end, left_flank, right_flank, dna_seq] = rows[0]
if protein_seq is None:
protein_seq = ""
if left_flank is None:
left_flank = ""
if right_flank is None:
right_flank = ""
if dna_seq is None:
dna_seq = ""
return [exon_seq_id, protein_seq, pepseq_transl_start, pepseq_transl_end, left_flank, right_flank, dna_seq]
def stable2gene (cursor, stable_id=None, db_name=None):
if (not stable_id):
return 0
if (db_name and not switch_to_db(cursor, db_name)):
return False
qry = "select gene_id from gene where stable_id='%s'" % stable_id
rows = search_db (cursor, qry, verbose = False)
if (not rows):
rows = search_db (cursor, qry, verbose = True)
return 0
return int(rows[0][0])
def check_ccds(cursor, transcript_stable_id="", transcript_id=""):
ccds = ""
qry = "select dna_align_feature.hit_name "
qry += "from dna_align_feature, transcript, transcript_supporting_feature "
qry += " where dna_align_feature.dna_align_feature_id = transcript_supporting_feature.feature_id "
qry += " and transcript_supporting_feature.feature_type ='dna_align_feature' "
qry += " and transcript_supporting_feature.transcript_id =transcript.transcript_id "
if transcript_stable_id:
qry += " and transcript.stable_id = '%s' " % transcript_stable_id
elif transcript_id:
qry += " and transcript.transcript_id = '%s' " % transcript_id
else:
return ccds
rows = search_db(cursor, qry)
if not rows:
return ccds
for row in rows:
if "CCDS" in row[0]:
ccds = row[0]
return ccds
def get_predicted_exons(cursor, gene_id, species):
exons = []
# get the region on the gene
ret = get_gene_region(cursor, gene_id)
if ret:
[gene_seq_id, gene_region_start, gene_region_end, gene_region_strand] = ret
else:
print "region not retrived for ", species, gene_id
return []
qry = "SELECT * FROM prediction_exon WHERE seq_region_id = %d " % gene_seq_id
qry += " AND seq_region_start >= %d AND seq_region_start <= %d " % (gene_region_start, gene_region_end)
qry += " AND seq_region_end >= %d AND seq_region_end <= %d " % (gene_region_start, gene_region_end)
rows = search_db(cursor, qry)
if not rows:
return []
for row in rows:
exon = Exon()
exon.gene_id = gene_id
exon.load_from_ensembl_prediction(gene_region_start, gene_region_end, row)
exons.append(exon)
return exons
def get_exon_seq_by_db_id (cursor, exon_seq_id, db_name=None):
if (db_name):
if not switch_to_db(cursor, db_name):
return False
qry = "select exon_seq_id, protein_seq, pepseq_transl_start, pepseq_transl_end, "
qry += " left_flank, right_flank, dna_seq "
qry += " from exon_seq where exon_seq_id = %d" % exon_seq_id
rows = search_db(cursor, qry)
if (not rows):
#rows = search_db(cursor, qry, verbose = True)
return []
[exon_seq_id, protein_seq, pepseq_transl_start,
pepseq_transl_end, left_flank, right_flank, dna_seq] = rows[0]
if (protein_seq is None):
protein_seq = ""
if (left_flank is None):
left_flank = ""
if (right_flank is None):
right_flank = ""
if (dna_seq is None):
dna_seq = ""
return [exon_seq_id, protein_seq, pepseq_transl_start, pepseq_transl_end, left_flank, right_flank, dna_seq]
def find_mammals(cursor, trivial_name_list):
mammals = []
for trivial_name in trivial_name_list:
switch_to_db(cursor, get_compara_name(cursor))
tax_id = trivial2taxid(cursor, trivial_name)
parent_id = taxid2parentid(cursor, tax_id)
tax_id = parent_id
is_mammal = False
while tax_id:
qry = "select name_txt from names where tax_id= %d " % int(tax_id)
qry += " and name_class = 'scientific name'"
rows = search_db(cursor, qry)
if rows and rows[0][0]:
if 'mammal' in rows[0][0].lower():
is_mammal = True
break
elif 'vertebrat' in rows[0][0].lower():
# if the thing wasa mammal, we would have found it by now
is_mammal = False
break
parent_id = taxid2parentid(cursor, tax_id)
if parent_id and parent_id > 1:
tax_id = parent_id
else:
tax_id = None
if is_mammal:
mammals.append(trivial_name)
return mammals
def check_ccds (cursor, transcript_stable_id = "", transcript_id = ""):
ccds = ""
qry = "select dna_align_feature.hit_name "
qry += "from dna_align_feature, transcript, transcript_supporting_feature "
qry += " where dna_align_feature.dna_align_feature_id = transcript_supporting_feature.feature_id "
qry += " and transcript_supporting_feature.feature_type ='dna_align_feature' "
qry += " and transcript_supporting_feature.transcript_id =transcript.transcript_id "
if (transcript_stable_id):
qry += " and transcript.stable_id = '%s' " % transcript_stable_id
elif (transcript_id):
qry += " and transcript.transcript_id = '%s' " % transcript_id
else:
return ccds
rows = search_db(cursor, qry)
if not rows:
return ccds
for row in rows:
if 'CCDS' in row[0]:
ccds = row[0]
return ccds
def stable2gene(cursor, stable_id=None, db_name=None):
if not stable_id:
return 0
if db_name and not switch_to_db(cursor, db_name):
return False
qry = "select gene_id from gene where stable_id='%s'" % stable_id
rows = search_db(cursor, qry, verbose=False)
if not rows:
rows = search_db(cursor, qry, verbose=True)
return 0
return int(rows[0][0])
def get_common_name(cursor, species):
switch_to_db(cursor, get_compara_name(cursor))
tax_id = species2taxid(cursor, species)
switch_to_db(cursor, get_ncbi_tax_name(cursor))
qry = "select name_txt from names where "
qry += "tax_id = %d and " % tax_id
qry += "name_class = 'genbank common name'"
rows = search_db(cursor, qry)
if rows:
if ('ERROR' in rows[0]):
search_db(cursor, qry, verbose=True)
return ""
else:
return rows[0][0]
return ""
def get_common_name (cursor, species):
switch_to_db(cursor, get_compara_name(cursor))
tax_id = species2taxid (cursor, species)
switch_to_db(cursor,get_ncbi_tax_name (cursor))
qry = "select name_txt from names where "
qry += "tax_id = %d and " % tax_id
qry += "name_class = 'genbank common name'"
rows = search_db (cursor, qry)
if rows:
if ('ERROR' in rows[0]):
search_db (cursor, qry, verbose = True)
return ""
else:
return rows[0][0]
return ""
def get_gene_coordinates(cursor, gene_id, db_name=None):
if db_name:
if not switch_to_db(cursor, db_name):
return None
qry = "select seq_region_id, seq_region_start, seq_region_end, seq_region_strand "
qry += " from gene "
qry += " where gene_id = %d" % gene_id
rows = search_db(cursor, qry)
if not rows or isinstance(rows[0], str) and "error" in rows[0].lower():
search_db(cursor, qry, verbose=True)
return None
return rows[0]
def get_predicted_exons (cursor, gene_id, species):
exons = []
# get the region on the gene
ret = get_gene_region (cursor, gene_id)
if ret:
[gene_seq_id, gene_region_start, gene_region_end,
gene_region_strand] = ret
else:
print "region not retrived for ", species, gene_id
return []
qry = "SELECT * FROM prediction_exon WHERE seq_region_id = %d " % gene_seq_id
qry += " AND seq_region_start >= %d AND seq_region_start <= %d " % \
(gene_region_start, gene_region_end)
qry += " AND seq_region_end >= %d AND seq_region_end <= %d " % \
(gene_region_start, gene_region_end)
rows = search_db (cursor, qry)
if (not rows):
return []
for row in rows:
exon = Exon()
exon.gene_id = gene_id
exon.load_from_ensembl_prediction (gene_region_start, gene_region_end, row)
exons.append(exon)
return exons
def find_mammals(cursor, trivial_name_list):
mammals = []
for trivial_name in trivial_name_list:
switch_to_db(cursor, get_compara_name(cursor))
tax_id = trivial2taxid (cursor, trivial_name)
parent_id = taxid2parentid (cursor, tax_id)
tax_id = parent_id
is_mammal = False
while tax_id:
qry = "select name_txt from names where tax_id= %d " % int(tax_id)
qry += " and name_class = 'scientific name'";
rows = search_db (cursor, qry)
if rows and rows[0][0]:
if 'mammal' in rows[0][0].lower():
is_mammal = True
break
elif 'vertebrat' in rows[0][0].lower():
# if the thing wasa mammal, we would have found it by now
is_mammal = False
break
parent_id = taxid2parentid (cursor, tax_id)
if parent_id and parent_id>1:
tax_id = parent_id
else:
tax_id = None
if is_mammal:
mammals.append(trivial_name)
return mammals
def get_gene_coordinates (cursor, gene_id, db_name=None):
if (db_name):
if not switch_to_db(cursor, db_name):
return None
qry = "select seq_region_id, seq_region_start, seq_region_end, seq_region_strand "
qry += " from gene "
qry += " where gene_id = %d" % gene_id
rows = search_db (cursor, qry)
if ( not rows or isinstance(rows[0], str) and 'error' in rows[0].lower()):
search_db (cursor, qry, verbose = True)
return None
return rows[0]
def get_canonical_transcript_id (cursor, gene_id, db_name=None):
if db_name and not switch_to_db(cursor, db_name):
return []
qry = "select canonical_transcript_id"
qry += " from gene where gene_id=%d" % gene_id
rows = search_db (cursor, qry, verbose=False)
if (not rows):
rows = search_db (cursor, qry, verbose=True)
return ""
elif ( 'Error' in rows[0]):
print rows[0]
return ""
return rows[0][0]
def get_gene_region (cursor, gene_id, is_known=None):
qry = "select seq_region_id, seq_region_start, seq_region_end, "
qry += " seq_region_strand "
qry += " from gene where gene_id=%d" % gene_id
if (not is_known is None and is_known):
qry += " and status='known' "
rows = search_db (cursor, qry, verbose=False)
if (not rows):
rows = search_db (cursor, qry, verbose=True)
return []
elif ( 'Error' in rows[0]):
print rows[0]
return []
return rows[0]
def get_compara_name (cursor):
# find the release number
qry = "select value from exolocator_config.parameter where name = 'ensembl_release_number'"
rows = search_db(cursor, qry)
if not rows or 'error' in rows[0][0].lower():
print 'ensembl_release_number not set in exolocator_config'
exit(1)
release_number = rows[0][0]
qry = "show databases like '%compara_{0}%'".format(release_number)
rows = search_db (cursor, qry)
if (not rows):
rows = search_db (cursor, qry, verbose = True)
return ""
return rows[0][0]
def get_gene_region(cursor, gene_id, is_known=None):
qry = "select seq_region_id, seq_region_start, seq_region_end, "
qry += " seq_region_strand "
qry += " from gene where gene_id=%d" % gene_id
if not is_known is None and is_known:
qry += " and status='known' "
rows = search_db(cursor, qry, verbose=False)
if not rows:
rows = search_db(cursor, qry, verbose=True)
return []
elif "Error" in rows[0]:
print rows[0]
return []
return rows[0]
