Added cohort test

tests/test_cohort.py

@@ -1,37 +1,28 @@
-'''
 import unittest
 from cohorts import Cohort
 
-class TestCohortMethods(object):
-
-
-	def __init__(self):
+top = "./"
+data_dirs = { 'my_cohort' : top+"data/" }
+file_dirs = { 'my_cohort' : top+"sample_data/" }
+replicates_files = { 'my_cohort' : "df_replicates.tsv" }
+#sample_files = { 'my_cohort' : "df_samples.tsv" }
+sample_groups_files = { 'my_cohort' : "df_sample_groups.tsv" }
+cohort = { 'my_cohort' : 'my_cohort' }
+references = { 'my_cohort' : 'ref' }
+treatments = { 'my_cohort' : 'trt' }
+cohort_name = 'my_cohort'
+c = Cohort(cohort=cohort[cohort_name],marker_type="protein",
+					data_dir=data_dirs[cohort_name],file_dir=file_dirs[cohort_name],
+					replicates_file=replicates_files[cohort_name],
+					#sample_files=sample_files[cohort],
+					sample_groups_file=sample_groups_files[cohort_name],
+					reference=references[cohort_name],
+					treatment=treatments[cohort_name])
 
-		top = "./"
-		data_dirs = { 'my_cohort' : top+"data/" }
-		file_dirs = { 'my_cohort' : top+"sample_data/" }
-		replicates_files = { 'my_cohort' : "df_replicates.tsv" }
-		#sample_files = { 'my_cohort' : "df_samples.tsv" }
-		sample_groups_files = { 'my_cohort' : "df_sample_groups.tsv" }
-		cohort = { 'my_cohort' : 'my_cohort' }
-		references = { 'my_cohort' : 'ref' }
-		treatments = { 'my_cohort' : 'trt' }
-		cohort_name = 'my_cohort'
-		c = Cohort(cohort=cohort[cohort_name],marker_type="protein",
-							data_dir=data_dirs[cohort_name],file_dir=file_dirs[cohort_name],
-							replicates_file=replicates_files[cohort_name],
-							#sample_files=sample_files[cohort],
-							sample_groups_file=sample_groups_files[cohort_name],
-							reference=references[cohort_name],
-							treatment=treatments[cohort_name])
-
-		self.cohort = c
+class TestCohortMethods(object):
 
 	def test_cohort_name(self):
-		return self.cohort.cohort=='my_cohort'
+		return c.cohort=='my_cohort'
 
 if __name__ == '__main__':
-	unittest.main()
-'''
-def given():
-	return True
+	unittest.main()