def getWholeGenomById(id_whole_genome):
"""
get a whole genome according to it id
:param id_whole_genome: Id of the whole genome
:type id_whole_genome: int
:return: whole genome Object
:rtype WholeDNA
"""
wholeDNAObj = WholeDNA.get_whole_dna_by_id(id_whole_genome)
return wholeDNAObj
for contig_element in list_contig_name:
contig_obj = Contig(head=contig_element, sequence='')
list_cnt.append(contig_obj)
#id_contig = -1, id_contig_db_outside = -1, head = "", sequence = " ", fk_id_whole_genome = -1
print(list_cnt)
list_of_proteins = xls_obj.create_proteins_from_file()
qty_proteins_loaded = len(list_of_proteins)
qty_contigs_loaded = xls_obj.get_number_different_contigs()
print(qty_contigs_loaded)
print(qty_proteins_loaded)
#Test empty WHole Genome
#, id_wholeDNA = -1, head = "", head_id = "", sequence = ""
whole_dna_obj = WholeDNA(head="Unknown",
head_id="Unknown",
sequence="Unknown")
whole_dna_obj.create_whole_dna_no_verification()
#Create an organism:
#id_organism, gi, acc_num, qty_proteins, assembled, qty_contig, fk_source = -1, fk_strain = -1, fk_type = -1, fk_whole_genome = -1, fk_source_data = "NULL"
gi_name = "Greg_" + strain_obj.designation
acc_value = "Greg_" + strain_obj.designation
id_strain = strain_obj.id_strain
print("insert the Whole DNA")
id_whole_genom = whole_dna_obj.id_wholeDNA
fk_type_organism = -1
if "_phi" not in file_name or "phage" not in file_name:
fk_type_organism = 1