def load_toxoplasma_mutant(raw_data, row):
# move down to attribute count
row += 1
attribute_count = int(raw_data[row][1])
toxoplasma_mutant_list = []
if attribute_count > 0:
row += 1
for i in range(0, attribute_count):
# move down to data
row += 1
name = raw_data[row][0]
name = name[1:-1]
target_name = raw_data[row][1]
target_name = target_name[1:-1]
background = raw_data[row][2]
background = background[1:-1]
selection = raw_data[row][3]
selection = selection[1:-1]
mutation_type = raw_data[row][4]
mutation_type = mutation_type[1:-1]
promoter = raw_data[row][5]
promoter = promoter[1:-1]
organism = raw_data[row][6]
organism = organism[1:-1]
target_gene = raw_data[row][7]
target_gene = target_gene[1:-1]
# load organism
organism = importer_organism.get_organism(organism)
# load ontology term
background = importer_ontology.get_ontology_term(
"toxoplasma mutant", "toxoplasma mutant background", background
) # get ontology term
selection = importer_ontology.get_ontology_term(
"toxoplasma mutant", "toxoplasma mutant selection", selection
) # get ontology term
mutation_type = importer_ontology.get_ontology_term(
"toxoplasma mutant", "toxoplasma mutant mutation type", mutation_type
) # get ontology term
promoter = importer_ontology.get_ontology_term(
"toxoplasma mutant", "toxoplasma mutant promoter", promoter
) # get ontology term
# load of Genes
if target_gene:
target_gene = importer_gene.get_gene(target_gene)
if (
name
and target_name
and background
and selection
and mutation_type
and promoter
and organism
and target_gene
):
toxoplasma_mutant = importer_toxoplasma_mutant.get_toxoplasma_mutant_with_target_gene(
name, target_name, background, selection, mutation_type, promoter, organism, target_gene
) # return toxoplasma mutant
toxoplasma_mutant_list.append(toxoplasma_mutant)
elif name and target_name and background and selection and mutation_type and promoter and organism:
toxoplasma_mutant = importer_toxoplasma_mutant.get_toxoplasma_mutant_without_target_gene(
name, target_name, background, selection, mutation_type, promoter, organism
) # return toxoplasma mutant
toxoplasma_mutant_list.append(toxoplasma_mutant)
return toxoplasma_mutant_list
def load_antibody(raw_data, row):
# move down to attribute count
row += 1
attribute_count = int(raw_data[row][1])
antibody_list = []
if attribute_count > 0:
row += 1
for i in range(0, attribute_count):
# move down to data
row += 1
name = raw_data[row][0]
name = name[1:-1]
target_name = raw_data[row][1]
target_name = target_name[1:-1]
tagged = raw_data[row][2]
tagged = tagged[1:-1]
tag_target = raw_data[row][3]
tag_target = tag_target[1:-1]
source = raw_data[row][4]
source = source[1:-1]
catalog_number = raw_data[row][5]
catalog_number = catalog_number[1:-1]
epitope = raw_data[row][6]
epitope = epitope[1:-1]
lot_number = raw_data[row][7]
lot_number = lot_number[1:-1]
ifa_localization = raw_data[row][8]
ifa_localization = ifa_localization[1:-1]
chip_peaks = raw_data[row][9]
chip_peaks = chip_peaks[1:-1]
monoclonal = raw_data[row][10]
monoclonal = monoclonal[1:-1]
isotype = raw_data[row][11]
isotype = isotype[1:-1]
immunogen_source = raw_data[row][12]
immunogen_source = immunogen_source[1:-1]
conjugation = raw_data[row][13]
conjugation = conjugation[1:-1]
validated = raw_data[row][14]
validated = validated[1:-1]
url = raw_data[row][15]
url = url[1:-1]
animal_host = raw_data[row][16]
animal_host = animal_host[1:-1]
target_gene = raw_data[row][17]
target_gene = target_gene[1:-1]
# load ontology term
animal_host = importer_ontology.get_ontology_term(
"antibody", "antibody host organism", animal_host
) # get ontology term
# load of Genes
if target_gene:
target_gene = importer_gene.get_gene(target_gene)
if name and target_name and target_gene:
antibody = importer_antibody.get_antibody_with_target_gene(
name,
target_name,
tagged,
tag_target,
source,
catalog_number,
epitope,
lot_number,
ifa_localization,
chip_peaks,
monoclonal,
isotype,
immunogen_source,
conjugation,
validated,
url,
animal_host,
target_gene,
) # return antibody
antibody_list.append(antibody)
elif name and target_name:
antibody = importer_antibody.get_antibody_without_target_gene(
name,
target_name,
tagged,
tag_target,
source,
catalog_number,
epitope,
lot_number,
ifa_localization,
chip_peaks,
monoclonal,
isotype,
immunogen_source,
conjugation,
validated,
url,
animal_host,
) # return antibody
antibody_list.append(antibody)
return antibody_list
