def test_format_map_file(self):
"""format_map_file should produce correct result"""
desc_key = "Description"
sample_id = "SampleID"
headers = ['SampleID', 'a', 'Description', 'b']
id_map = {'x': {'a': 3, 'b': 4}, 'y': {'a': 5, 'b': 6}}
desc_map = {'x': 'sample x', 'y': 'sample y'}
run_desc = 'run desc'
self.assertEqual(
format_map_file(headers, id_map, desc_key, sample_id, desc_map,
run_desc), """#SampleID\ta\tb\tDescription
#run desc
x\t3\t4\tsample x
y\t5\t6\tsample y""")
def test_format_map_file(self):
"""format_map_file should produce correct result"""
desc_key = "Description"
sample_id = "SampleID"
headers = ['SampleID', 'a', 'Description', 'b']
id_map = {'x':{'a':3,'b':4}, 'y':{'a':5,'b':6}}
desc_map = {'x':'sample x','y':'sample y'}
run_desc = 'run desc'
self.assertEqual(format_map_file(headers, id_map, desc_key, sample_id,\
desc_map, run_desc),
"""#SampleID\ta\tb\tDescription
#run desc
x\t3\t4\tsample x
y\t5\t6\tsample y""")
def test_format_map_file(self):
"""format_map_file should produce correct result"""
desc_key = "Description"
sample_id = "SampleID"
headers = ["SampleID", "a", "Description", "b"]
id_map = {"x": {"a": 3, "b": 4}, "y": {"a": 5, "b": 6}}
desc_map = {"x": "sample x", "y": "sample y"}
run_desc = "run desc"
self.assertEqual(
format_map_file(headers, id_map, desc_key, sample_id, desc_map, run_desc),
"""#SampleID\ta\tb\tDescription
#run desc
x\t3\t4\tsample x
y\t5\t6\tsample y""",
)
def write_corrected_file(headers, id_map, description_map, run_description, \
output_filepath, chars_replaced=False):
""" Writes corrected mapping file with illegal characters replaced """
outf = open(output_filepath, 'w')
if chars_replaced:
outfile_data=format_map_file(headers, id_map, DESC_KEY, SAMPLE_ID_KEY,\
description_map, run_description)
else:
outfile_data="# No invalid characters were found and replaced.\n"+\
"# Note that non-IUPAC DNA characters found in primer or barcode\n"+\
"# sequences are not replaced but will be listed in the .log file."
for data in outfile_data:
outf.write(data)
return
def write_corrected_file(headers, id_map, description_map, run_description, output_filepath, chars_replaced=False):
""" Writes corrected mapping file with illegal characters replaced """
outf = open(output_filepath, "w")
if chars_replaced:
outfile_data = format_map_file(headers, id_map, DESC_KEY, SAMPLE_ID_KEY, description_map, run_description)
else:
outfile_data = (
"# No invalid characters were found and replaced.\n"
+ "# Note that non-IUPAC DNA characters found in primer or barcode\n"
+ "# sequences are not replaced but will be listed in the .log file."
)
for data in outfile_data:
outf.write(data)
return
