def createContigNew(contigObj, bacteriumId):
head_cnt = ''
if '>' not in contigObj.head:
head_cnt = '>' + contigObj.head
else:
head_cnt = contigObj.head
contigObj = Contig(id_contig_db_outside = contigObj.id_contig_db_outside, head = head_cnt, sequence = contigObj.sequence)
idContig = createContig(contigObj, bacteriumId)
return idContig
def getContigsByOrganis(idOrganism):
"""
get all the contigs of a given Organism
:param idOrganism: Id of the organism
:type idOrganism: int
:return: list of contigs
:rtype list[Contig]
"""
listContigs = []
qtyContigs = 0
listContigs = Contig.get_all_Contigs_by_organism_id(idOrganism)
return listContigs
def insertBacteriumProteinsWholeDNAContigsNopositions(bacteriumObj, idStrainAPI, wholeDNAObj, dictProts, dictConts):
"""
insert the bacterium, the whole genome, the contigs, the proteins, and the genes without protein s contig positions
:param bacteriumObj: Organism object (old DB)
:param idStrainAPI: id of the strain on the new DB (API)
:param wholeDNAObj: Whole Genome object (old DB)
:param dictProts: Dict with the proteins Key: id of the contig - Value: list of proteins (old DB)
:param dictConts: Dict with the contigs Key: id of the contig - Value: contig object (old DB)
:type bacteriumObj: Organism_new
:type idStrainAPI: int
:type wholeDNAObj: WholeDNA_new
:type dictProts: dictionary{int: list[Proteins]}
:type dictConts: dictionary{int: Contig}
:return: matrix with all the data
:rtype panda dataframe
"""
#Test contigs
list_contigs = Contig.get_all_Contigs_by_organism_id(bacteriumObj.id_organism)
contigs_validation = testContigContainDNA(list_contigs)
if contigs_validation == True:
bacteriumCreatedID = createBacterium(bacteriumObj, idStrainAPI)
wholeDNACreatedID = createWholeDNA(wholeDNAObj, bacteriumCreatedID)
for contig in list_contigs:
print('Hello')
contigID = createContigNew(contig, bacteriumCreatedID)
for key,proteinlist in dictProts.items():
for protein in proteinlist:
createProtein(protein, bacteriumCreatedID, None)
print('Hello')