def select_all_score_blast_p_all_attributes(self):
"""
return all the blast scores in the database
:return: cursor with all scores blast
:rtype Cursor list
"""
sql_string = "SELECT id_blast_FSB_P, pident_FSB_P, length_FSB_P, mismatch_FSB_P, gapopen_FSB_P, pstart_FSB_P, pend_FSB_P, bstart_FSB_P, bend_FSB_P, evalue_FSB_P, bitscore_FSB_P, plen_FSB_P, blen_FSB_P, FK_id_PPI_couple_PCP_FSB_P FROM F_SCORE_BLAST_P"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_dataset_conf_ds(self):
"""
return all the connections dataset_conf_dataset
:return: cursor with all sources dataset_conf_dataset
:rtype Cursor list
"""
sql_string = "SELECT id_ds_conf_ds_DCD, value_config_DCD, FK_id_configuration_DCT_DCD, FK_id_dataset_DS_DCD FROM DATASET_CONF_DS"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_prodom_all_attributes(self):
"""
return all the PROT_DOM in the database
:return: cursor with all domains
:rtype Cursor list
"""
sql_string = "SELECT id_prot_dom_DP, FK_id_protein_PT_DP, FK_id_domain_DO_DP FROM PROT_DOM"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_domain_interaction_by_pfam(self, pfam_designation):
"""
return all the DDI interactions in the DOMINE database given a pfam
:return: cursor with all DDI
:rtype Cursor list
"""
sql_string = "select DISTINCT Domain1, Domain2, iPfam, 3did, ME, RCDP, Pvalue, Fusion, DPEA, PE, GPE, DIPD, RDFF, KGIDDI, INSITE, DomainGA, PP, PredictionConfidence, SameGO from INTERACTION Where Domain1 LIKE '" + str(pfam_designation) + "%' or Domain2 LIKE '" + str(pfam_designation) + "%'"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_LT_all_attributes(self):
"""
return all the lysis type in the database
:return: cursor with all lysis type
:rtype Cursor list
"""
sql_strin = "SELECT * FROM LYSIS_TYPE"
dalObj = DAL(self.da_name, sql_strin)
results = dalObj.executeSelect()
return results
def select_all_cogs_all_attributes(self):
"""
return all the cogs in the database
:return: cursor with all cogs
:rtype Cursor list
"""
sql_string = "SELECT * FROM COGS"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def get_all_interactions(self):
"""
return all the interactions as in INTERACTION table in DOMINE database
:return: cursor with all domains
:rtype Cursor list
"""
sql_string = "select Domain1, Domain2, iPfam, 3did, ME, RCDP, Pvalue, Fusion, DPEA, PE, GPE, DIPD, RDFF, KGIDDI, INSITE, DomainGA, PP, PredictionConfidence, SameGO from INTERACTION"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def get_all_domains(self):
"""
return all the domains in the database DOMINE. Return only the id (PFXXXXX)
:return: cursor with all domains
:rtype Cursor list
"""
sql_string = "select DomainAcc from PFAM"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_domains_ds_all_attributes(self):
"""
return all the Domains_ds configurations in the database
:return: cursor with all domains_ds
:rtype Cursor list
"""
sql_string = "SELECT id_domains_ds_DD, range_DD, auto_split_DD, nomralization_data_DD, FK_id_configuration_CF_DD, FK_id_user_US_DD FROM DOMAINS_DS"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_ddi_interactions_by_db(self, Fk_id_DB):
"""
return all the DDI in the database by an DB FK
:return: cursor with all DDI
:rtype Cursor list
"""
sql_string = "select id_DDI_inter_DD, FK_domain_a_DD, FK_domain_b_DD from DDI_INTERACTIONS, DDI_INTERACTIONS_DB Where id_DDI_inter_DD = FK_id_interaction_DD_DDB and FK_id_db_interaction_DDB = " + str(Fk_id_DB)
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_Datasets_conf_type(self):
"""
return all the connections dataset configurations types
:return: cursor with all types of configurations
:rtype Cursor list
"""
sql_string = "SELECT id_configuration_DCT, designation_DCT FROM DATASET_CONFIGURATIONS_TYPES"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_ddi_interactions(self):
"""
return all the DDI in the database
:return: cursor with all DDI
:rtype Cursor list
"""
sql_string = "SELECT id_DDI_inter_DD, FK_domain_a_DD, FK_domain_b_DD FROM DDI_INTERACTIONS"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_pfam_interactions_by_pfam(self, pfam_designation):
"""
return all the pfam interactions in the PFAM database given a pfam
:return: cursor with all pfam interactions
:rtype Cursor list
"""
sql_string = "select DISTINCT * from pfamA_interactions Where pfamA_acc_A = '" + str(pfam_designation) + "' or pfamA_acc_B = '" + str(pfam_designation) + "'"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_pfam_interactions(self):
"""
return all the pfam interactions in the database PFAM
:return: cursor with all pfam interactions
:rtype Cursor list
"""
sql_string = "SELECT * FROM pfamA_interactions"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def get_all_pfam_acc(self):
"""
return all the pfam in the database PFAM. Return only tha ACC
:return: cursor with all pfam interactions
:rtype Cursor list
"""
sql_string = "SELECT DISTINCT pfamA_acc FROM pfamA"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_typesOr_all_attributes(self):
"""
return all the Type_organism in the database
:return: cursor with all Type_organism
:rtype Cursor list
"""
sql_string = "SELECT * FROM TYPE_ORGANISM"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_datasets_all_attributes(self):
"""
return all the Datasets in the database
:return: cursor with all datasets
:rtype Cursor list
"""
sql_string = "SELECT id_dataset_DS, date_time_creation_DS, name_DS, FK_id_user_US_DS FROM DATASETS"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_cogprot_all_attributes(self):
"""
return all the COGS_PROT in the database
:return: cursor with all COGS_prots
:rtype Cursor list
"""
sql_string = "SELECT id_cog_prot_CP, FK_id_cog_CO_CP, FK_id_protein_PT_CP FROM COGS_PROT"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_bloc_score_domain(self):
"""
return all the domains score bloc in the database
:return: cursor with all domains score bloc
:rtype Cursor list
"""
sql_string = "SELECT score_dom_bloc_id_FSD, designation_FSD, date_creation_FSD FROM F_SCORE_DOMAINS_BLOC"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def get_all_score_domain_by_bloc_fk_id(self, fk_bloc_id):
"""
return all the Score_domain in the database
:return: cursor with all score_domain
:rtype Cursor list
"""
sql_string = "SELECT score_dom_id_SD, score_ddi_SD, FK_score_dom_bloc_FSD_SD, FK_prot_dom_bact_DP_SD, FK_prot_dom_phage_DP_SD, FK_couple_CP_SD FROM SCORE_DOMAIN WHERE FK_score_dom_bloc_FSD_SD = " + str(fk_bloc_id)
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_wholeDNAs_all_attributes(self):
"""
Consult the DB and return a list with all WHOLE_DNA objects with all details
:return: cursor with all WHOLE_DNA
:rtype Cursor list
"""
sql_string = "SELECT * FROM WHOLE_DNA"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def get_whole_dna_by_id(self, id_whole_dna):
"""
Get a Whole_DNA by its id
:return: Whole_DNA elements info
:rtype List(infos Whole_DNA)
"""
sql_string = "SELECT id_dna_WD, head_WD, head_id_WD, sequence_WD FROM WHOLE_DNA WHERE id_dna_WD = " + str(id_whole_dna)
dalobj = DAL(self.db_name, sql_string)
results = dalobj.executeSelect()
return results[0]
def select_all_interaction_type_all_attributes(self):
"""
return all the interactions type in the database
:return: cursor with all Interactions Types
:rtype Cursor list
"""
sql_string = "SELECT id_type_inter_IT, designation_IT FROM INTERACTIONS_TYPES"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def get_family_by_id(self, id_genus):
"""
Get a family by its id
:return: Family elements info
:rtype List(infos family)
"""
sql_string = "SELECT id_family_FA, designation_FA FROM FAMILIES WHERE id_family_FA = " + str(id_genus)
dalobj = DAL(self.db_name, sql_string)
results = dalobj.executeSelect()
return results[0]
def select_all_contigs_all_attributesby_fk_whole_dna(self, fk_whole_dna):
"""
Consult the DB and return a list with contigs which have a FK_whole_DNA
:return: cursor with the contigs
:rtype Cursor list
"""
sql_string = "SELECT id_contig_CT, id_contig_db_outside_CT, head_CT, sequence_CT, FK_id_whole_genome_WD_CT FROM CONTIGS WHERE FK_id_whole_genome_WD_CT = " + str(
fk_whole_dna)
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_proteins_all_attributes(self):
"""
return all the Proteins in the database
:return: cursor with all proteins
:rtype Cursor list
"""
sql_string = "SELECT id_protein_PT, id_protein_BD_online_PT, designation_PT, sequence_PT, DNA_sequence_PT, start_point_PT, end_point_PT, start_point_cnt_PT, end_point_cnt_PT, FK_id_contig_CT_PT FROM PROTEINS"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_proteins_all_attributes_by_organism_id(self, id_organism):
"""
Consult the DB and return a list with proteins from an organism id
:return: cursor with the proteins
:rtype Cursor list
"""
sql_string = "SELECT id_protein_PT, id_protein_BD_online_PT, designation_PT, sequence_PT, DNA_sequence_PT, start_point_PT, end_point_PT, start_point_cnt_PT, end_point_cnt_PT, FK_id_contig_CT_PT FROM PROTEINS, GENES WHERE id_protein_PT = FK_id_protein_PT_GE and FK_id_organism_OR_GE = " + str(
id_organism)
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_proteins_all_attributes_by_fk_contig(self, fk_contig):
"""
Consult the DB and return a list with proteins which have a fk_contig
:return: cursor with the proteins
:rtype Cursor list
"""
sql_string = "SELECT id_protein_PT, id_protein_BD_online_PT, designation_PT, sequence_PT, DNA_sequence_PT, start_point_PT, end_point_PT, start_point_cnt_PT, end_point_cnt_PT, FK_id_contig_CT_PT FROM PROTEINS WHERE FK_id_contig_CT_PT = " + str(
fk_contig)
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_couples_all_attributes(self):
"""
return all the Couples in the database
:return: cursor with all couples
:rtype Cursor list
"""
sql_string = "SELECT id_couple_CP, interaction_CP, FK_id_organism_bact_OR_CP, FK_id_organism_phage_OR_CP, FK_id_type_inter_IT_CP, FK_id_level_LI_CP, FK_id_lysis_LT_CP, FK_source_couple_SD_CP FROM COUPLES"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results
def select_all_level_interactions_all_attributes(self):
"""
return all the Level interaction in the database
:return: cursor with all Leve interaction
:rtype Cursor list
"""
sql_string = "SELECT id_level_LI, designation_LI FROM LEVEL_INTERACTIONS"
dalObj = DAL(self.db_name, sql_string)
results = dalObj.executeSelect()
return results