def get_dna_seq(query):
""" displays DNA seq associated with the query"""
dna_seq = DB.get_gene_entry(query)["DNA_seq"]
if not dna_seq.isalpha():
raise TypeError("Not valid")
else:
return dna_seq
def get_coding_seq(query):
"""
displays the coding region
Parameters: query, type string
Ouput: CDS
"""
coord = DB.get_gene_entry(query)['CDS']
coding_seq = get_dna_seq(query)[coord[0] - 1:coord[1]]
return coding_seq
def get_aminoacid_seq(query):
""" displays the amino acid sequence
parameters: query, type st
ring
returns the amino acid sequence"""
amino_acid_seq = DB.get_gene_entry(query)["aminoacid_sequence"]
if not amino_acid_seq.isalpha(
): #checks if all characters in the string are alphabets
raise TypeError("Not valid")
else:
return amino_acid_seq
def get_CDS_coord(query):
"""
displays the coordinates of CDS
:return: a list of lists containing pairs of 2 coordinates
"""
valid = False
cds_coord = DB.get_gene_entry(query)['CDS']
for coord in cds_coord:
if type(coord) == int and coord > 0:
valid = True
if valid == True:
return cds_coord
else:
raise TypeError("Not valid")
def non_coding_dna_seq(query):
"""
retrieves the non coding DNA sequence downstream and upstream of the coding region
:param query:
:return: non_coding_seq type string
"""
non_coding_seq = ''
whole_dna_seq = get_dna_seq(query)
coord = DB.get_gene_entry(query)['CDS']
start = coord[0]
end = coord[1]
upstream_non_coding = whole_dna_seq[0:(start - 1)]
downstream_non_coding = whole_dna_seq[(end - 1):len(whole_dna_seq) - 1]
non_coding_seq = non_coding_seq + upstream_non_coding + " " + downstream_non_coding
return non_coding_seq
def by_genbank_identifier(genBank_id):
return DB.get_gene_entry()
def by_chromosomal_loc(chromosomal_loc):
return DB.get_gene_entry()
def by_protein_product(protein_name):
return DB.get_gene_entry()
def by_accession_code(accession_code):
return DB.get_gene_entry()