def cufflinks_gene_diff_import(experiment_id, filename):
'''This function imports the data from a gene_exp.diff into :class:`~data.models.GeneExperimentData` objects.
This function requires a valid experiment_id and a file.
'''
import decimal
experiment = mRNASeqExperiment.objects.get(pk=experiment_id)
new_genes = 0
updated_genes = 0
with open(filename, 'r') as inputfile:
for row in csv.DictReader(inputfile, delimiter='\t'):
try:
datum = GeneExperimentData(
experiment=experiment,
gene=Gene.objects.get(pk=row['gene']),
fold_change=row['log2(fold_change)'],
p_value=row['p_value'],
q_value=row['q_value'],
locus=row['locus'],
internal_id=row['test_id'],
sample_1=row['sample_1'],
sample_2=row['sample_2'],
amount_1=row['value_1'],
amount_2=row['value_2'],
status=row['status'],
test_statistic=row['test_stat'],
significant=row['significant'])
datum.save()
updated_genes += 1
except Gene.DoesNotExist:
#create a new gene with that name
new_gene = Gene(name=row['gene'])
new_gene.save()
datum = GeneExperimentData(
experiment=experiment,
gene=new_gene,
fold_change=row['log2(fold_change)'],
p_value=row['p_value'],
q_value=row['q_value'],
locus=row['locus'],
internal_id=row['test_id'],
sample_1=row['sample_1'],
sample_2=row['sample_2'],
amount_1=row['value_1'],
amount_2=row['value_2'],
status=row['status'],
test_statistic=row['test_stat'],
significant=row['significant'])
datum.save()
new_genes += 1
return "Added %i measurements and created %i new genes." % (
updated_genes + new_genes, new_genes)
def test_gene_experiment_datum_unicode(self):
'''This tests the unicode representation of a :class:`~data.models.GeneExperimentData`.'''
test_datum = GeneExperimentData(
experiment=mRNASeqExperiment.objects.get(pk=1),
gene=Gene.objects.get(pk='Pikfyve'),
fold_change=0.419048218,
p_value=0.110512214,
q_value=0.995959851)
self.assertEqual(test_datum.__unicode__(), "Pikfyve")
def test_create_new_gene_experiment_datum_minimum(self):
'''This test creates a :class:`~data.models.GeneExperimentData` with the required information only.'''
test_datum = GeneExperimentData(
experiment=mRNASeqExperiment.objects.get(pk=1),
gene=Gene.objects.get(pk='Pikfyve'),
fold_change=0.419048218,
p_value=0.110512214,
q_value=0.995959851)
test_datum.save()
self.assertEqual(test_datum.pk,
1) #presumes no objects loaded in fixture data
def test_create_new_gene_experiment_datum_all(self):
'''This test creates a :class:`~data.models.GeneExperimentData` with all information entered.'''
test_datum = GeneExperimentData(
experiment=mRNASeqExperiment.objects.get(pk=1),
gene=Gene.objects.get(pk='Pikfyve'),
fold_change=0.419048218,
p_value=0.110512214,
q_value=0.995959851,
locus='1:3054232-3054733',
internal_id='XLOC_000001',
sample_1='Control',
sample_2='Treated',
amount_1=0.0778978,
amount_2=0.0881688,
status='OK',
test_statistic=-0.0754818,
significant='no')
test_datum.save()
self.assertEqual(test_datum.pk,
1) #presumes one model loaded in fixture data
