def test_merge_mapping_correct_num_records(self):
"""merge_mapping_file: num recs returned is correct with varied input
"""
# number of lines is always 1 greater than number of samples, and number
# of tab-separated fields on each line is equal
actual = merge_mapping_files([self.m1])
self.assertEqual(len(actual),3)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),1)
actual = merge_mapping_files([self.m2])
self.assertEqual(len(actual),2)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),1)
actual = merge_mapping_files([self.m3])
self.assertEqual(len(actual),4)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),1)
actual = merge_mapping_files([self.m1,self.m2])
self.assertEqual(len(actual),4)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),1)
actual = merge_mapping_files([self.m1,self.m3])
self.assertEqual(len(actual),6)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),1)
actual = merge_mapping_files([self.m2,self.m3])
self.assertEqual(len(actual),5)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),1)
actual = merge_mapping_files([self.m1,self.m2,self.m3])
self.assertEqual(len(actual),7)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),1)
actual = merge_mapping_files([self.m3,self.m3,self.m3,self.m3])
self.assertEqual(len(actual),4)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),1)
def write_full_mapping_file(study, study_input_dir,zip_fname,files_to_remove,
output_dir):
""" Generate a merged mapping file """
# write per_run mapping files and then return the prefixes
run_prefixes=write_db_mapping_files(study,True,study_input_dir,False)
# define the full mapping file
mapping_fname='study_%s_mapping_file.txt' % (str(study))
final_mapping_fp=join(output_dir,mapping_fname)
# add to list of files to remove
files_to_remove.append(final_mapping_fp)
# iterate over run_prefixes and create a list of files that need to be
# merged
mapping_files_to_merge=[]
for i in run_prefixes:
mapping_fp=join(study_input_dir,'study_%s_run_%s_mapping.txt' % \
(str(study),str(i)))
# add to list of files to remove
files_to_remove.append(mapping_fp)
mapping_files_to_merge.append(open(mapping_fp,'U'))
# merge the mapping files and return tabular data
mapping_data = merge_mapping_files(mapping_files_to_merge,\
no_data_value='no_data')
# write the full mapping file
write_mapping_file(mapping_data,final_mapping_fp)
# zip the full mapping file
#cmd_call='cd %s; tar czvf %s %s' % (study_input_dir,zip_fname,mapping_fname)
#system(cmd_call)
return files_to_remove
def test_merge_mapping_file_good_duplicates(self):
"""merge_mapping_file: same sample ids merged correctly when they have mergable data
"""
actual = merge_mapping_files([self.m1,self.m1_dup_good])
# 2 total entries
self.assertEqual(len(actual),3)
# all fields are the same length
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),1)
# 7 fields
self.assertEqual(len(actual[0].split('\t')),7)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
verbose = opts.verbose
output_fp = opts.output_fp
mapping_files = [open(fp,'U') for fp in opts.mapping_fps]
no_data_value = opts.no_data_value
mapping_data = merge_mapping_files(mapping_files,\
no_data_value=no_data_value)
write_mapping_file(mapping_data,output_fp)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
verbose = opts.verbose
output_fp = opts.output_fp
mapping_files = [open(fp, 'U') for fp in opts.mapping_fps]
no_data_value = opts.no_data_value
mapping_data = merge_mapping_files(mapping_files,
no_data_value=no_data_value)
write_mapping_file(mapping_data, output_fp)
def test_merge_mapping_file_good_duplicates(self):
"""merge_mapping_file: same sample ids merged correctly when they have mergable data
"""
actual = merge_mapping_files([self.m1, self.m1_dup_good])
# 2 total entries
self.assertEqual(len(actual), 3)
# all fields are the same length
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),
1)
# 7 fields
self.assertEqual(len(actual[0].split('\t')), 7)
def test_merge_mapping_file(self):
"""merge_mapping_file: functions with default parameters """
actual = merge_mapping_files([self.m1, self.m2, self.m3])
expected = self.m1_m2_m3_exp
self.assertTrue(actual[0].startswith('#SampleID\tBarcodeSequence'))
self.assertTrue(actual[0].endswith('Description'))
actual.sort()
expected.sort()
for a, e in zip(actual, expected):
a_fields = a.split('\t')
e_fields = e.split('\t')
a_fields.sort()
e_fields.sort()
self.assertEqual(a_fields, e_fields)
def test_merge_mapping_file(self):
"""merge_mapping_file: functions with default parameters """
actual = merge_mapping_files([self.m1,self.m2,self.m3])
expected = self.m1_m2_m3_exp
self.assertTrue(actual[0].startswith('#SampleID\tBarcodeSequence'))
self.assertTrue(actual[0].endswith('Description'))
actual.sort()
expected.sort()
for a,e in zip(actual,expected):
a_fields = a.split('\t')
e_fields = e.split('\t')
a_fields.sort()
e_fields.sort()
self.assertEqual(a_fields,e_fields)
def test_merge_mapping_correct_num_records(self):
"""merge_mapping_file: num recs returned is correct with varied input
"""
# number of lines is always 1 greater than number of samples, and number
# of tab-separated fields on each line is equal
actual = merge_mapping_files([self.m1])
self.assertEqual(len(actual), 3)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),
1)
actual = merge_mapping_files([self.m2])
self.assertEqual(len(actual), 2)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),
1)
actual = merge_mapping_files([self.m3])
self.assertEqual(len(actual), 4)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),
1)
actual = merge_mapping_files([self.m1, self.m2])
self.assertEqual(len(actual), 4)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),
1)
actual = merge_mapping_files([self.m1, self.m3])
self.assertEqual(len(actual), 6)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),
1)
actual = merge_mapping_files([self.m2, self.m3])
self.assertEqual(len(actual), 5)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),
1)
actual = merge_mapping_files([self.m1, self.m2, self.m3])
self.assertEqual(len(actual), 7)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),
1)
actual = merge_mapping_files([self.m3, self.m3, self.m3, self.m3])
self.assertEqual(len(actual), 4)
self.assertEqual(len(set([len(line.split('\t')) for line in actual])),
1)
def test_merge_mapping_correct_num_records(self):
"""merge_mapping_file: num recs returned is correct with varied input
"""
# length is always number of samples plus 1 (for header line)
actual = merge_mapping_files([self.m1])
self.assertEqual(len(actual), 3)
actual = merge_mapping_files([self.m2])
self.assertEqual(len(actual), 2)
actual = merge_mapping_files([self.m3])
self.assertEqual(len(actual), 4)
actual = merge_mapping_files([self.m1, self.m2])
self.assertEqual(len(actual), 4)
actual = merge_mapping_files([self.m1, self.m3])
self.assertEqual(len(actual), 6)
actual = merge_mapping_files([self.m2, self.m3])
self.assertEqual(len(actual), 5)
actual = merge_mapping_files([self.m1, self.m2, self.m3])
self.assertEqual(len(actual), 7)
actual = merge_mapping_files([self.m3, self.m3, self.m3, self.m3])
self.assertEqual(len(actual), 13)
def test_merge_mapping_correct_num_records(self):
"""merge_mapping_file: num recs returned is correct with varied input
"""
# length is always number of samples plus 1 (for header line)
actual = merge_mapping_files([self.m1])
self.assertEqual(len(actual),3)
actual = merge_mapping_files([self.m2])
self.assertEqual(len(actual),2)
actual = merge_mapping_files([self.m3])
self.assertEqual(len(actual),4)
actual = merge_mapping_files([self.m1,self.m2])
self.assertEqual(len(actual),4)
actual = merge_mapping_files([self.m1,self.m3])
self.assertEqual(len(actual),6)
actual = merge_mapping_files([self.m2,self.m3])
self.assertEqual(len(actual),5)
actual = merge_mapping_files([self.m1,self.m2,self.m3])
self.assertEqual(len(actual),7)
actual = merge_mapping_files([self.m3,self.m3,self.m3,self.m3])
self.assertEqual(len(actual),13)
def test_merge_mapping_file_dups(self):
"""merge_mapping_file: duplicate sample ids stay duplicate """
actual = merge_mapping_files([self.m1, self.m2, self.m1])
# length is number of samples plus header line
self.assertEqual(len(actual), 6)
def test_merge_mapping_file_dups(self):
"""merge_mapping_file: duplicate sample ids stay duplicate """
actual = merge_mapping_files([self.m1,self.m2,self.m1])
# length is number of samples plus header line
self.assertEqual(len(actual),6)
