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BUG: Fix issue #271 #291

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Sep 6, 2014
Merged

BUG: Fix issue #271 #291

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bc0b27d
BUG: Fix problem with unique/single valued-columns
ElDeveloper Sep 5, 2014
fa232fd
TST: Add three more test cases related to #271
ElDeveloper Sep 5, 2014
76da557
DOC: Add note about the fix of #271
ElDeveloper Sep 6, 2014
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1 change: 1 addition & 0 deletions ChangeLog.md
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ Emperor 0.9.3-dev (changes since Emperor 0.9.2 go here)

* Fixed problem where coordinate files with large values (greater than 100) would not be displayed on screen.
* Fixed problem that prevented the user from scrolling through the categories in the user interface.
* Fixed problem that removed unique/single-valued categories in the mapping file even if these were selected with `--color_by`.
* Clean-up the layout of the user interface so it's cleaner and consistent.
* Fix problem where long category names would alter the layout of the interface.
* Fix inability to write an 'E' character in the Filename field when exporting an svg.
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17 changes: 10 additions & 7 deletions emperor/util.py
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Expand Up @@ -146,20 +146,23 @@ def preprocess_mapping_file(data, headers, columns, unique=False, single=False,
line.append(''.join([line[index] for index in indices]))
headers.append(new_column)

# remove all unique or singled valued columns
# remove all unique or singled valued columns that are not included in
# the list of categories that should be kept i. e. columns
if unique or single:
columns_to_remove = []
metadata = MetadataMap(mapping_file_to_dict(data, headers), [])

# find columns that have values that are all unique
if unique == True:
columns_to_remove += [column_name for column_name in headers[1::]
if metadata.hasUniqueCategoryValues(column_name)]
if unique:
for c in headers[1::]:
if metadata.hasUniqueCategoryValues(c) and c not in columns:
columns_to_remove.append(c)

# remove categories where there is only one value
if single == True:
columns_to_remove += [column_name for column_name in headers[1::]
if metadata.hasSingleCategoryValue(column_name)]
if single:
for c in headers[1::]:
if metadata.hasSingleCategoryValue(c) and c not in columns:
columns_to_remove.append(c)
columns_to_remove = list(set(columns_to_remove))

# remove the single or unique columns
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46 changes: 43 additions & 3 deletions tests/test_util.py
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Expand Up @@ -121,8 +121,8 @@ def test_preprocess_mapping_file(self):

# check it removes columns with unique values
out_data, out_headers = preprocess_mapping_file(self.mapping_file_data,
self.mapping_file_headers, ['SampleID', 'BarcodeSequence',
'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description'],
self.mapping_file_headers, ['SampleID', 'LinkerPrimerSequence',
'Treatment', 'DOB'],
unique=True)
self.assertEquals(out_headers, ['SampleID', 'LinkerPrimerSequence',
'Treatment', 'DOB'])
Expand All @@ -131,7 +131,7 @@ def test_preprocess_mapping_file(self):
# check it removes columns where there is only one value
out_data, out_headers = preprocess_mapping_file(self.mapping_file_data,
self.mapping_file_headers, ['SampleID', 'BarcodeSequence',
'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description'],
'Treatment', 'DOB', 'Description'],
single=True)
self.assertEquals(out_headers,['SampleID', 'BarcodeSequence',
'Treatment', 'DOB', 'Description'])
Expand All @@ -151,6 +151,32 @@ def test_preprocess_mapping_file(self):
self.assertEquals(out_data, MAPPING_FILE_DATA_DUPLICATED)
self.assertEquals(out_headers, ['SampleID', 'Treatment', 'DOB'])

# check it doesn't remove columns because all are included in the list
out_data, out_headers = preprocess_mapping_file(self.mapping_file_data,
self.mapping_file_headers, ['SampleID', 'BarcodeSequence',
'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description'],
unique=True)
self.assertEquals(out_headers, ['SampleID', 'BarcodeSequence',
'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description'])
self.assertEquals(out_data, MAPPING_FILE_DATA_CAT_G)

# check it doesn't remove columns because all are included in the list
out_data, out_headers = preprocess_mapping_file(self.mapping_file_data,
self.mapping_file_headers, ['SampleID', 'BarcodeSequence',
'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description'],
single=True)
self.assertEquals(out_headers, ['SampleID', 'BarcodeSequence',
'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description'])
self.assertEquals(out_data, MAPPING_FILE_DATA_CAT_G)

# check it doesn't remove columns because all are included in the list
out_data, out_headers = preprocess_mapping_file(self.mapping_file_data,
self.mapping_file_headers, ['SampleID', 'BarcodeSequence',
'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description'],
unique=True, single=True)
self.assertEquals(out_headers, ['SampleID', 'BarcodeSequence',
'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description'])
self.assertEquals(out_data, MAPPING_FILE_DATA_CAT_G)

def test_keep_columns_from_mapping_file(self):
"""Check correct selection of metadata is being done"""
Expand Down Expand Up @@ -438,6 +464,20 @@ def test_sanitize_mapping_file(self):
['PC.635', 'Fast', 'Fast20080116'],
['PC.636', 'Fast', 'Fast20080116']]

MAPPING_FILE_DATA_CAT_G = [['PC.354', 'AGCACGAGCCTA', 'YATGCTGCCTCCCGTAGGAGT',
'Control', '20061218', 'Control_mouse_I.D._354'], ['PC.355', 'AACTCGTCGATG',
'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218', 'Control_mouse_I.D._355'],
['PC.356', 'ACAGACCACTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061126',
'Control_mouse_I.D._356'], ['PC.481', 'ACCAGCGACTAG', 'YATGCTGCCTCCCGTAGGAGT',
'Control', '20070314', 'Control_mouse_I.D._481'], ['PC.593', 'AGCAGCACTTGT',
'YATGCTGCCTCCCGTAGGAGT', 'Control', '20071210', 'Control_mouse_I.D._593'],
['PC.607', 'AACTGTGCGTAC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20071112',
'Fasting_mouse_I.D._607'], ['PC.634', 'ACAGAGTCGGCT', 'YATGCTGCCTCCCGTAGGAGT',
'Fast', '20080116', 'Fasting_mouse_I.D._634'], ['PC.635', 'ACCGCAGAGTCA',
'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116', 'Fasting_mouse_I.D._635'],
['PC.636', 'ACGGTGAGTGTC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116',
'Fasting_mouse_I.D._636']]

MAPPING_FILE_DATA_GRADIENT = [
['PC.354', 'Control','3', '40', 'Control20061218'],
['PC.355', 'Control','9', '44', 'Control20061218'],
Expand Down