def create_Samples_from_header(line):
"""Creates sample objects for input file.
It uses CN and CP input lists from users.
It creates a sample object for each one containing the name
and the column index for genotype, depth amd var/depth (ratio) columns
"""
samples_name_list = []
sample_return_list = []
geno_sufix = '.replicate1_Genotype'
depth_sufix = '.replicate1_Depth'
ratio_sufix = '.replicate1_Var/Depth'
consequence = 'Variant_effect'
columns = line.split('|')
for i in columns:
res = re.search('(.*)\.replicate1_Genotype$', i)
if res: samples_name_list.append(res.group(1))
for sample_name in samples_name_list:
genotype_col = columns.index(sample_name+geno_sufix)
depth_col = columns.index(sample_name+depth_sufix)
ratio_col = columns.index(sample_name+ratio_sufix)
#We get consequence column
consequence_col = columns.index(consequence)
#We create the sample object
new_sample = Sample(sample_name, genotype_col, depth_col, ratio_col)
#We set the consequence column
new_sample.set_consequence_col(consequence_col)
#We create and set a ConsequenceCounter object to the Sample.
consequence_counter = ConsequenceCounter()
#We set the ConsequenceCounter object to Sample object
new_sample.set_consequence_counter(consequence_counter)
sample_return_list.append(new_sample)
return sample_return_list
